Copyright: © Waters Corporation 2003


Help Contents
Contents

Inlets Introduction

Introduction

The Inlet Editor

The Inlet Editor Toolbar

The Short Cut bar

The System Status Page

Multi Inlet Status View

Inlet Configuration

Events and Triggering Wizard

Preparation Methods

Waters Systems

Instrument Control Option Pack

Acquity UPLC

Waters 2777

Waters 600 Pump

Waters 2690/2695 Autosampler

Waters 2690/2695 Pump

Waters 996 PDA Detector

Waters 486 UV Detector

Waters 2487 UV Detector

Waters 2487 IEEE Detector

Waters SAT/IN PDA Detector

Waters 2700 Autosampler

Waters 2790/2795 Autosampler

Waters 2790/2795 Pump

Waters 2796 Status Pages

Waters 2796 Pump

Waters 2796 Autosampler

Waters 2796 Menu

Waters CapLC System Status Pages

Waters CapLC Pump

Waters CapLC Autosampler

Waters CapLC PDA Detector

Waters CapLC Plumbing Diagrams

Waters 515 and 1525 Pumps

Agilent Systems

Hewlett Packard 5890 Gas Chromatograph

Hewlett Packard 7673A Auto Injector

Hewlett Packard HPLC Systems

Hewlett Packard 1100 G1367A Well Plate Autosampler

The HP Diode Array Detector

The HP6890 GC Control

Gilson Systems

Introduction

Gilson Configuration Pages

Gilson Pump

Gilson UV Detector

Jasco Systems

Jasco 900 and Jasco 1500 Autosamplers

Jasco 900 and Jasco 1500 Pumps

Jasco 900 and Jasco 1500 UV Detectors

Shimadzu

Shimadzu Autosamplers

Shimadzu Pump

Shimadzu UV Detectors

LC Packings

Introduction

UltiMate Pump

Famos Autosampler

UV Detector

CE Instruments

CE Instruments GC8000 Gas Chromatograph

CE Instruments AS800 Auto Injector

CTC and Others

CTC A200S Autosampler

CTC PAL Autosampler

Cetac ASX100 Autosampler

Cetac ASX500 Autosampler

Solids Probe

DCI Probe

Thermospray Probe

RoboProbe

Contact Closure


Inlets Introduction - Introduction
Introduction

Mass spectrometers are usually used in conjunction with an inlet system such as a liquid chromatograph (LC) or a gas chromatograph (GC). MassLynx can control this equipment during data acquisition to provide complete control of an experiment. Autosamplers will often be used to automate the running of samples.

More:

Inlets


Inlets

There are a wide range of Inlets available with MassLynx, these are selected using the Inlet Configuration  wizard (see page 5).

The method used to control the inlet system is set up before you start to acquire any data and is saved on disk for use by the acquisition system. Different methods can be saved, accessible by name in the usual manner. You must supply the name of the inlet method that you wish to use when you start an acquisition by entering it into the 'Inlet' field in either the Single or Multiple sample start editors (these are covered in the next section).

N.B. Make sure that any changes that you make to an inlet program are saved to disk before you start an acquisition. This is done by selecting the Save option on the File menu of the inlet editor or by pressing the [image] toolbar button. If you do not save the parameters then the previous ones will be used as MassLynx reads the parameters from disk, not from the editor, when it starts to acquire. Iconising the display does not save the parameters but you will be given the option to save any changes that you have made if you actually close the editor.

Note. For older Transputer based machines select Configure, Select Interface, GC or LC system (ACE) from the Acquisition Control Panel to enable the Inlet Configuration  wizard. The list of inlet options that appears in the Select Interface dialog reflects the inlet systems, which were selected when MassLynx was installed. To change an Inlet for other non ACE systems MassLynx will need to be re-installed to gain access to the control software for the new inlet system. These inlets will not be available to Non-Transputer based Instruments e.g. CE Instruments (Chapter 3).

Note. For Transputer based instruments acquisitions that use an inlet system, can only be started from the Instrument Control Panel and cannot be started from the tune page.

More:

Autosamplers


Autosamplers

An autosampler can only be used with the Sample List Editor on the MassLynx top level screen.

The rules regarding the saving of parameters for inlet editors apply to autosampler editors as well.


The Inlet Editor

The Inlet Editor supports a number of instrument configurations. An instrument configuration is set up when MassLynx is installed but alternative configurations can be selected from within the editor itself. A configuration generally consists of a HPLC or GC (i.e., an Inlet), an Autosampler and a Detector (either UV or PDA). However, it is also possible to have a dual detector configuration using a SAT/IN analogue input box. Corresponding to these components the Inlet Editor provides three main windows (four for a dual detector set-up) referred to as views. There is also a status view for displaying information concerning the actual instruments. Only one view can be displayed at any one time which is selected by menu or toolbar button. Each main view may consist of one or more sub-views or pages, which are selected by a tab, and it is on these pages that the user enters method parameters (unless it is a status view). Alternatively, if multiple-inlet support is enabled then up to 8 pumps and 8 detectors can be configured to run alongside a single Autosampler.

A particular instrument control software implementation provides the views (and pages) discussed in the previous paragraph. These views are described later on this manual in the chapters for the relevant instruments.

In summary the Inlet Editor is used to:-

•	View the status of the current system.

•	Define the GC or LC, autosampler and detector methods.

•	Change instrument configuration

•	Control pumps and lamps and run methods.

Click on the Inlet Editor button, shown bellow, on the MassLynx Shortcut bar,

or select Methods, Inlet from the Acquisition Control Panel menu bar.

More:

MassLynx Options


MassLynx Options

The Inlet Editor requires some settings to be selected in the MassLynx Options dialog, which is invoked from the MassLynx Shortcut bar.

The following options are relevant to the Inlet Editor: -

Allow Random Bottle Access	This switches the capability to have non-sequential vial references in a sample list when on a MUX system.
Multi-Inlet Capability	This puts the inlet system into multi inlet mode and allows the user to select a number of parallel inlets.
Number of Parallel Inlets	A number of parallel inlets from 2-8.
Sample Prep	Ticking this allows multiple inlets to be used on a non-MUX system using a prep file.


The Inlet Editor Toolbar

The toolbar is displayed across the top of the application window, below the menu bar. The toolbar provides quick mouse access to many tools used in the control software, the buttons have the following actions.

The exact appearance of the toolbar will vary depending upon the installed configuration. Details of specific toolbar buttons are given in the Instrument Guides.

	Create a New method.
	Open an existing method.
	Save the method with its current name.
	Print the current method.
	Display the System Status dialog.
	Edit Inlet system parameters.
	Edit Autosampler parameters.
	Edit Detector parameters.
	Start or stop the pump.
	Turn Lamp on and off.
	Run the currently saved method.
	Load the currently saved method.
 Related Topics


The Short Cut bar

Figure 1 The Inlet Editor Short Cut bar

The Short Cut bar allows for quick and easy access to the System Status Page and the setup pages for the pump, autosampler and detector.

 Related Topics


The System Status Page

The System Status page displays information about the state of the machine being controlled. This page can be accessed within the Inlet Editor by selecting View, Status from the menu bar or by pressing the [image] toolbar button.

Note: This changes for a GC, see HP6890. The Waters Cap LC also has a different System Status page see the Waters Cap LC System Status Page.

Indicators	The Running, Pump On and Injector Cycle indicators at the left-hand side of the screen give you information on the current status of the LC system. The OK and Ready Indicators become illuminated in red if the LC System has an error. You can then click on the red indicators to give you more information on the cause of the malfunction.
Run Time	Displays how long the method has been running.
Flow Rate	This is the current flow rate as returned by the instrument.
Pressure	Displays the current pressure in the instrument.
Column Left and Column Right	Displays the current temperature of the left and right columns. These will be grayed out if column heaters are not installed.
Sample Temp	Displays the current temperature of the sample. This will be grayed out if a sample heater is not installed.
Gradient	Displays the solvent percentages at which the LC System is currently operating.
PDA Detector	When acquiring diode array data the Diode Array Status displays the number of scans currently acquired.


Multi Inlet Status View

The Multi Inlet Status view appears on tabbed pages. The first page of which represents the overall system status. The other pages are functionally identical to the page described in The System Status Page and display the status for each pump connected, on a 1 to 1 relationship. There is a page (Status 1, Status 2 etc) for each pump that is configured.

More:

Indicators

Pump Status

Saving and Loading LC Parameter Files

To Print an LC Method Report

To Download Parameters to the LC System

To Run the Pump with Initial Conditions

To Turn on the Lamp

To Begin a Gradient Method or Start an Injection


Indicators

Running Indicator	Colored yellow when a method is running on any of the instruments, otherwise colored gray.
Pump on Indicator	Colored yellow when flow is on in any of the LC systems, otherwise colored gray.
Injector Cycle Indicator	Colored yellow when the Autosampler is carrying out an injection or is performing some other operation such as washing the needle. Otherwise colored gray.
Ready Indicator	Colored red if the system is not ready, otherwise colored yellow.
OK Indicator	Colored red if there is an error any all of the connected systems or there has been a communication error on any of the systems, otherwise colored green. If there is a communication error all other indicators are colored gray.


Pump Status

These represent each connected LC system's OK indicator. These duplicate the OK indicators on each of the status pages


Saving and Loading LC Parameter Files

The Current LC parameters can be saved to disk by choosing Save or Save As from the Inlet Editor File menu.

A set of previously saved LC parameters can be recalled from disk by choosing Open from the Inlet Editor File menu.


To Print an LC Method Report

Choose Print from the Inlet Editor File menu or press the [image] toolbar button. Press OK to print a report detailing the parameters used in the current LC Method.


To Download Parameters to the LC System

To download the parameters to the LC system, press the [image] button or choose Load Method from the LC menu.

The status bar will indicate the progress of downloading the parameters. Once values have been downloaded you can start the pump running with the initial conditions.


To Run the Pump with Initial Conditions

Select Pump On from the LC menu or click on the [image] button. The pump will begin running with its initial conditions.


To Turn on the Lamp

Select Lamp On from the LC menu or click on the [image] button.


To Begin a Gradient Method or Start an Injection

You can run a single injection with the Autosampler by selecting Run Method from the LC menu as soon as the menu item is enabled (it is disabled when the system is running a method). If a method is already running in the LC System it will not be possible to start a new method (either inject or run gradient only) until the previous method has stopped.

Selecting Run Method (No Injection) from the LC menu starts the gradient (if entered) to allow manual injections.


Inlet Configuration

The Inlet Configuration dialog shows the current setup of Inlets, Autosamplers and detectors.

Multiple Inlets are only shown if Multi-Inlet Capability has been selected in the Mass Lynx Options dialog.

More:

Adding Pumps, Autosamplers and Detectors


Adding Pumps, Autosamplers and Detectors

•	To access the dialog select Tools, Instrument Configuration from the Inlet Editor menu.

•	To change the current setup, highlight a line in the list and select Configure to invoke the Inlet Configuration Wizard.

The Wizard dynamically restricts the choices available, based upon the selections made. To add an Inlet, Autosampler and Detector: -

1.	On the Configuration Wizard Welcome page follow the on screen instructions. Click Next

2.	Select the required pump from the Select Pump dialog Click Next.

3.	Select the required autosampler from the Select Autosampler dialog (this is similar in appearance to the Select Pump dialog). This dialog will show only the autosamplers that are compatible with the chosen pump. Click Next.

4.	Select the required detector from the Select Detector dialog. This dialog will show only the detectors that are compatible with the chosen pump and autosampler. Click Next.

5.	Depending on the configuration selected the HPIB Communication or GPIB Communication dialogs are invoked. After filling out the values, if needed Click Next.

6.	The Configuration Successful dialog is displayed. Click Finish, this returns to the Inlet Configuration dialog

More:

HPIB Communication

GPIB Communication


HPIB Communication

When an Instrument configuration has been selected on the Instrument tab default device addresses are written to this dialog. Values can be changed if required. For the HP1100 DAD detector the PC Connection should be set to HP100 DAD.


GPIB Communication

When an Instrument configuration has been selected on the Instrument tab default IDs are written to this dialog. These may need changing and will be defined on setup by a Micromass engineer. For more information consult the relevant instrument instruction manual.


Events and Triggering Wizard

This wizard is for configuring input and output events and triggering methods for certain pumps and detectors.

1.	To invoke the Events and Triggering Wizard select the Events & Triggering button on the Instrument Configuration dialog, the Events and Triggering Welcome Page is displayed.Click Next.

2.	The Events page is displayed and can be used to configure input and output events such as triggering an acquisition on a Mass Spectrometer.Click Next

Note. The Events page is only available on non Transputer instruments.

Input Events	When acquiring from the sample list, the acquisition will not commence until a contact closure is seen on the specified port.
Output Events	These events are sent at the end of an acquisition from the sample list.
3.	The Triggering page is displayed and allows for triggering to selected by contact closure or by software.Click Next

4.	Note. Triggering allows the definition of how the LC or detector run is triggered, whether by contact closure or software.

5.	The end page is displayed. Either click Finish to accept the configuration or Back to change it.


Preparation Methods

When it is a requirement to run several pumps on a single spray system, this facility allows for the creation of an "Umbrella" method that will tie the various inlet methods for the pumps together. It is this method that is selected when running from the sample list

More:

New Prep Method

Edit Prep Method

View Prep Method


New Prep Method

If Sample Prep has been selected in the MassLynx Options dialog, the Prep Options menu will be available on the Inlet Editor Menu Bar. Selecting Prep options, New Prep Method will invoke the Prep Wizard.

•	Enter the name of the Method in the Edit box and Click next.

•	The next page allows the required method files to be put into the method. Choose the method from the drop down box, for each pump configuration.

•	Click Finish to close the Prep Wizard and return to the Inlet Editor.


Edit Prep Method

•	Existing Preparation Methods can be edited by selecting Prep Options, Edit Prep Method. This Invokes the Edit Method Page.

•	Choose the method from the drop down box and Click Next.

•	The Method Editor page is invoked with the currently selected methods showing in the drop down boxes. These methods can now be changed.


View Prep Method

To view a Preparation Method select Prep Options, View Prep Method, this works in a similar fashion to the Edit Prep Method option but Method Editor Page has all the drop down boxes disabled.


Instrument Control Option Pack

The following Instruments are installed with the Waters Instrument Control Option Pack (ICOP):

•	The Acquity System, Binary Solvent Manager, Sample Manager and TUV detector

•	Waters 2767 Sample Manager and Collector

•	Waters 2747 Sample Manager and Collector

•	Waters 2525 Pump

•	Waters 2488 IEEE Detector

When installed each instrument has its own Instrument Method window. The Inlet Method Editor only displays the status pages.

To Install:

1.	Select the modules required as normal in the Inlet Configuration wizard.

2.	Click Finish to close the wizard and open the Waters ICOP.

3.	Follow the on screen instructions and choose the instruments you wish to install.

4.	Click Finish when prompted to close the installer.


Acquity UPLC

The following instruments can be installed for UPLC:

•	Acquity Binary Solvent Manager

•	Acquity Sample Manager

•	Acquity TUV detector

•	Acquity PDA detector – the functionality of this is identical to the Waters 996 PDA detector.

Methods are set by opening the appropriate Instruments Method Editor from the Inlet Editor's shortcut bar.

Click [image] within the Method Editors for further help.

More:

Status Pages

Instrument Methods

Acquity Bed Layout

Plate Generator


Status Pages

In addition to the standard status tab there is an ACQUITY Additional Status tab.

This displays the control panels of the instruments. Key pump status is displayed and frequently used control and maintenance functions. This negates the need to access the Acquity console (which is also installed with ICOP) for all but the less frequent functions.

Note: The Acquity console should be accessed for more detailed monitoring of the system

More:

Acquity Binary Solvent Manager Status Panel

Acquity Sample Manager Status Panel

Acquity TUV Detector Status Panel


Acquity Binary Solvent Manager Status Panel

Click [image] to stop or start the flow of the Binary Solvent Manager.

The following status indicators are displayed:

•	Flow – this shows the actual flow rate in ml/min

•	Solvent Selections – displays the solvent selection for each pump

•	Composition – displays %A and %B

•	System Pressure – displays the pump pressure in psi

•	Progress – provides additional user feedback on the current operation in progress

Click on any of the indicators to open the Set Flow dialog box from which the Flow rate and solvent composition and selection can be edited.

Right-click on the Status panel to reveal a pop-up menu of frequently used functions:

•	Wet Prime – select this to open the A/B Solvents dialog box. Use this to choose the lines to prime, the solvents to prime with and the time the operation will take.

•	Prime/Stop Seal Wash

•	Reset BSM


Acquity Sample Manager Status Panel

Click [image] to open the Sample Manager.

The following status indicators are displayed:

•	Column Temperature

•	Sample Temperature

Click on any of the indicator to open the Set Temperature dialog box from which the temperatures can be altered.

Right-click on the Status panel to reveal a pop-up menu of frequently used functions:

•	Prime – select this to open the Prime Syringe dialog box, select Sample syringe or Sample Syringe and wash syringes and the Number of cycles

•	Wash needle – select this to open the Wash Needle dialog box. Select either Weak Wash or Strong Wash and enter a value in µL.

•	Set Lights

•	Reset SM

Further functionality has to be accessed from the Sample Manager Console.


Acquity TUV Detector Status Panel

Click [image] to open the TUV detector console for that instrument.

The following status indicators are displayed:

•	Absorbance Units

•	Wavelength

Click on the Wavelength indicators to open the Set Wavelength dialog box from which the wavelength can be altered.

Right-click on the Status panel to reveal a pop-up menu of frequently used functions:

•	Autozero

•	Reset TUV

Further functionality has to be accessed from the Sample Manger Console.


Instrument Methods

The following topics give recommended values and settings for Acquity method files.

More:

Acquity PDA Method

ACQUITY TUV Method


Acquity PDA Method

1.	Install the Acquity PDA detector with the Binary Solvent Manager and Sample Manager.

2.	Click Inlet to open the Binary Solvent Manager.

3.	Set the following parameters:

Run Time – 3.00 min

Solvents - dependant on sample.

Pressure Limits Low 0 psi

Pressure Limits High 15000 psi

Seal Wash 5.00 min

Se the gradient as shown in the table below:

	Time (min)	Flow mL/min	%A	%B	Curve
1	Initial	0.25	100.0	0.0
2	2.00	0.25	90	10.0	6
3	2.50	0.25	100.0	0.0t	6
4.	Click Detector and set the following PDA parameters:

5.	Select Autosampler to open the ACQUITY Sample Manager.

6.	Set the parameters as shown below:

7.	Select Advanced to open the Advanced Settings dialog box. Make sure that none of the options has been selected.

8.	Click OK.

9.	In the Inlet Editor, select File, Save As and save the method with an appropriate name.


ACQUITY TUV Method

1.	Install the Acquity TUV detector with the Binary Solvent Manager and Sample Manager.

2.	Click Inlet to open the Binary Solvent Manager.

3.	Set the following parameters:

Run Time – 3.00 min

Solvents - dependant on sample.

Pressure Limits Low 0 psi

Pressure Limits High 15000 psi

Seal Wash 5.00 min

Se the gradient as shown in the table below:

	Time (min)	Flow mL/min	%A	%B	Curve
1	Initial	0.25	100.0	0.0
2	2.00	0.25	90	10.0	6
3	2.50	0.25	100.0	0.0t	6
4.	Click Detector and set the following TUV parameters:

5.	Select Autosampler to open the ACQUITY Sample Manager.

6.	Set the parameters as shown below:

7.	Select Advanced to open the Advanced Settings dialog box. Make sure that none of the options has been selected.

8.	Click OK.

9.	In the Inlet Editor, select File, Save As and save the method with an appropriate name.


Acquity Bed Layout

The bed layout needs to be set before any method can be saved

Unlike other instruments, the Bed Layout is restricted to one Column with a minimum of two rows and maximum of 22 Rows.

To add extra rows:

1.	On the Bed Layout tab, add an integer between 2 and 22 in the right hand text box.

2.	Click [image] to enter the number.

3.	The Column is updated with the number of rows.

4.	Select Edit Plates on Layout to see each plate in the stack.

5.	Use the scroll bar to access all the configured plates. Double-clicking on a plate enables you to change the type of plate in that position.

There are a variety of default plates available, however, new plates can be added by the Plate Generator.


Waters Systems - Acquity UPLC - Plate Generator
Plate Generator

From the Inlet editor select Acquity Sampler, Plate Generator to display the Custom Rack Generator dialog box.

New plates can be created and the default ones modified.

New plates can be selected form the Bed Layout dialog box.

Rack Name	The name of the plate that is currently being edited.
Rows	The number of vials in a horizontal row and the distance between the center of one tube and the next tube in the same row. In the example plates below there are 4 rows.
Columns	The number of vials in a vertical column and the distance between the center of one tube and the next tube in the same column. In the example plates below there are 5 columns.
Vial	These parameters do not affect fraction collection.
Offsets	Allows alternate vial rows or columns to be offset.
Origin	The corner of the rack that the vial grid referencing starts from.
Grid Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Referencing	This has three options:  • XY which references the vials A1, B1 etc. • Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to right, then continues number the next row, right to left etc.
XY Referencing	Sequential Continuous	Sequential Discontinuous
Priority	Check the Horizontal First box if samples are to be acquired horizontally across the plate. If Referencing = X, Y, Horizontal = Letter, Vertical = Number and Horizontal Priority is checked, this will result in samples being acquired in the order A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired in the order 1A, 1B, 1C etc. If Referencing = sequential continuous or discontinuous and Horizontal Priority is checked, this will result in samples being acquired from row 1 then row 2. If the Horizontal Priority box is not checked samples will be acquired from column 1, then column 2 etc.
Plate Size	The size of the plate to its outside edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate.
More:

Creating and Deleting Plates


Creating and Deleting Plates

To create a custom rack, press the [image] button or select Rack, New Rack. This will create a new rack based on the Default Settings for New Rack described below, enter the appropriate values and press the save [image] button or select Rack, Save Current Rack.

To create a new rack based on an existing rack, display the existing rack, change the Rack Name, enter the appropriate values and press the save [image] button or select Rack, Save Current Rack.

The [image] and [image] toolbar buttons are used to page through the list of saved custom racks. The Previous Rack and Next Rack options on the Rack menu perform the same operation.

New racks are saved to the MassLynx Plates directory.

To delete a custom rack select the rack to delete, by typing the name in the Rack Name box or by paging through as above, and press the delete [image] button or choose Rack, Delete Current Rack.

Note: All of the spacings and the vial section are stored in 0.1mm units.


Waters 2777

Details for the Waters 2777 can be found under the  CTC PAL Autosampler.


Waters 600 Pump

The Waters 600 Pump pages can be accessed by selecting View, Waters600 Pump from the Inlet Editor menu bar, selecting Inlet from the short cut bar or by pressing the [image] toolbar button.

More:

Waters 600 Initial Conditions

Waters 600 Gradient Page

Waters 600 Initial Events Page

Waters 600 Programmed Events Page


Waters 600 Initial Conditions

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B, C and D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Solvent Name	Enter the name of the solvent that will be delivered through the corresponding Pump.
Flow Rate	This is the total flow rate of the solvent channels according to how you have configured the instrument.
Pressures	Enter the upper and lower limits of the pressure within the solvent delivery system (SDS) if the pressure falls outside of this range the SDS switches off.
Column Heater	If the instrument has an oven present then the column temperature can be set to a specified temperature in degrees centigrade. Enter the temperature to heat the column to in the Set box and a High Limit. If the temperature exceeds the High Limit then the system will shut down. If the software has been configured to operate without a column oven then these boxes will be grayed out.
Run Time	Enter the time in minutes that the method will run from the point of injection.
 Related Topics


Waters 600 Gradient Page

This page allows a gradient to be entered and edited. To operate in isocratic mode ensure that the timetable is empty.

To enable the B%, C% and/or D% boxes check the relevant boxes on the Initial Conditions page.

To add a gradient, enter a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient, click on a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes to the left of the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

Flow	Enter the flow rate for the solvent delivery system.
Curve	This sets the rate at which the solvent is to change to the new proportions and/or flow rates. See the Waters 600 Operator's Guide for a list of values.
 Related Topics


Waters 600 Initial Events Page

This page allows the initial state of switches 1 to 4 to be defined. Select from the drop down lists On, Off or No Change.

 Related Topics


Waters 600 Programmed Events Page

This page allows pump events to be entered and edited.

To add an event, type in a time, select an event from the drop down list box, select an action or enter a value and press the [image] toolbar button.

To delete a single event, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

 Related Topics


Waters 2690/2695 Autosampler

To control the Waters 2690/2695 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None.

More:

Waters 2690/2695 Toolbar

Waters 2690/2695 Autosampler Initial Conditions Page

Waters 2690/2695 Autosampler Purge Page


Waters 2690/2695 Toolbar

Two additional toolbar buttons are available for the Waters 2690/2695.

	Select to Wet Prime the Instrument
	Change Mode. Switch to local or remote mode.
 Related Topics


Waters 2690/2695 Autosampler Initial Conditions Page

This page is used to set parameters specific to the Sampler, to access it select View, Waters 2690/2695 AutoSampler, select Autosampler from the short cut bar or press the [image] toolbar button.

Sample Heater Temperature	If the sample heater is installed, enter the temperature that the sample should be to be heated or cooled to.  Range: 4.0 to 40.0 C.
Sample Heater Temperature Limit	Enter the maximum deviation in sample temperature allowed. If this is exceeded the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red.  Range: ±1.0 to ±20.0 C.
Injection Volume	Enter the volume of sample to be injected, in microlitres. Range: 0 to 2000 l. Note: If you are running from the Sample List, the injection volume in the sample list entry overrides the value entered here.
Needle Depth	This adjusts the depth of the needle tip to accommodate for sedimented samples or non-standard vials. A value of 0 corresponds to the bottom of the vial. Range: 0.0 to 20.0 mm in 0.1mm increments.
Draw Speed	This determines the rate in microlitres per second at which sample is extracted into the autosampler needle. It should be set according to the viscosity of the sample. Select one of Fast, Normal or Slow from the dropdown list box. The table below shows the draw rate for each selection using a 250 l syringe.
Selection	Draw Rate for a 250 l Syringe
Fast	5.0 l/sec
Normal	2.5 l/sec
Slow	1.0 l/sec
Optional Sample Loop	To inject sample volumes greater than 100 microlitres an additional sample loop can be installed (in series with the existing sample loop), check this box if an additional sample loop is used.
Vial number	The vial to inject from. Note: If a multisample acquisition is being run from the MassLynx Sample List, the Bottle # entry in the sample list overrides the value entered here.
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Waters 2690/2695 Autosampler Purge Page

This page is used to set the Autosampler purge volume, to access it click on the Autosampler Purge tab.

Loop Volumes	Enter the number of times the loop should be filled to purge the sample loop and syringe of traces of the previous sample. When set to a value greater than zero, this action is performed after every injection.
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Waters 2690/2695 Pump

Note: To control the Waters  2690/2695 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None. See Configuring the Inlet System in the Acquisition Control Panel chapter.

The Waters Pump pages can be accessed by selecting View, Waters 2690/2695 Pump from the Inlet Editor menu, selecting Inlet from the short cut bar or by pressing the [image] toolbar button.

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Waters 2690/2695 Solvents and Flows Page

Waters 2690/2695 Column Setup Page

Waters 2690/2695 Pump Gradient Page

Waters 2690/2695 Pump Events Page


Waters 2690/2695 Solvents and Flows Page

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must equal 100%. Solvent Names entered here will be displayed on the Pump Gradient page.
Pump A	This displays the remainder percentage after the solvent percentages have been set for the other enabled pumps.
Pump B, C and D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Run Time	This value is set to the time in minutes that the method will run from the point of injection.
Degasser	This value is set to the time in minutes that the method will run from the point of injection.
Flow	This is the total flow rate for the system.
Flow Ramp	Enter the time (in minutes) for the solvent delivery system to reach the maximum system flow rate (10 ml/min). Recommended minimum setting: 0.5 min.
 Related Topics


Waters 2690/2695 Column Setup Page

Column Heater Temperature	Enter the target operating temperature for the optional column heater. This value must be at least 5 C above ambient.  Range: 20 to 60 C.
Column Heater Temperature Limit	This is the maximum deviation in column temperature allowed. If this is exceeded the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red. Range: ±1 to ±20 C.
Low Pressure and High Pressure	Enter values as required. If the pressure falls outside these limits the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red. Low Pressure Range: 0 to 310 bar. Low Pressure Range: 0 to 345 bar.
Pre-column Volume	Enter the volume of solvent to pump through the column before an injection. Range: 1 to 10000 µl.
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Waters 2690/2695 Pump Gradient Page

This page allows a gradient to be entered and edited. If you wish to operate in isocratic mode then you should enter parameters on the Solvents and Flows page and ensure that the timetable is empty.

Time (mins)	Specifies the time at which the specified conditions (%A to %D, Flow, and Curve) for the row should take effect. Make sure you set Time for the first row to 0.00, to establish initial conditions for the gradient run. The range for rows other than row 1: 0.01 to 999.99 minutes
Solvent A %-Solvent D%	Specifies the percentage of solvent flow from each reservoir. For each row, the total of all solvents must equal 100%. Range: 0 to 100%.
Flow (ml/min)	Specifies the total flow rate for the solvent delivery system. Range: 1 to 10 ml/min.
Curve	This sets the rate at which the solvent is to change to the new proportions and/or flow rates. Curves are specified by number, available choices: 1 to 11 are shown in the table below and Curve profiles are shown in  Waters 2690/2695 Pump Gradient Page
Curve Number	Effect
1	Immediately goes to specified conditions
2 to 5	Convex
6	Linear
7 to 10	Concave
11	Maintains start condition until next step
Figure 2Curve Profiles

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Waters  2690/2695 Gradient Table Operation


Waters  2690/2695 Gradient Table Operation

To add a gradient, enter values in the relevant boxes and press the [image] toolbar button. You can add up to 15 rows to the table. Note: The first entry must have a time of 0.

To delete a single gradient, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

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Waters 2690/2695 Pump Events Page

This page allows pump events to be entered and edited.

Use the Event Table to program up to 16 events (both external and internal). The external events are triggered by four contact closures (relays) through output terminals (S1-S4) on the 2690/2695 Separations Module. The internal events are used to control the sample compartment temperature and column heater temperature, and to prime and flush the 2690/2695 Separations Module. Events can be triggered more than once and multiple events can be triggered simultaneously.

Time	Enter the time at which the event should start. Event rows are sorted automatically by time. Note: Different events can be programmed to occur at the same time. Range: 0.00 to 999.99 min.
Event	Enter the type of event signal required: one of the four TTL-level output switches (S1-S4), or one of the internal events (column heater temperature, sample compartment temperature or flush/prime). Available choices are shown below:-
•	Switch 1 to Switch 4 Corresponds to terminal strip positions S1 to S4 on the rear of the  2690/2695 module. Activating a Switch event triggers a contact closure for controlling an external device. After selecting a switch event, set a state for the switch by selecting On, Off, Toggle, Pulse Width or No Change. This state appears in the Action column of the table (refer to Switch States, below). Note: If Pulse is selected for a switch state, the duration of the pulse must be entered in the Width (min) field.

•	Set Temperature (Column or Sample) Specifies the temperature of an optional column heater, or an optional sample compartment heater/cooler. After selecting this event, select Column or Sample and enter the required Temperature in C. Note: When a Column Temperature event occurs, the temperature of the column heater changes from the value set in the Heaters and Pressures page to the value set for the event. When the event times out, the temperature changes back to the Heaters and Pressures page value. Column range: 20 to 60 C. Sample range: 4 to 40 C.

•	Flush/Prime Specifies a flush/prime operation for the 2690/2695 module. Use this event only when creating Inlet Pre-run and Inlet Post-run methods. These methods will use the solvent percentages and the run time from the Solvents and Flows page but will use the Flow value entered on this page. Note: The Time field is not accessible when you select a Flush/Prime event.

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Switch States

Waters 2690/2695 Event Table Operation


Switch States

•	On - Turns on a contact closure that triggers an external or internal event. With this function, the contact closure remains closed until an off function is sent.

•	Off - Turns off the contact closure for the event. With this function, the contact closure is broken.

•	Pulse - Transmits a single On/Off pulse. The contact closure is maintained for the number of seconds defined in the Value column. Range: 0.01 to 10.00 sec.

•	Toggle - Changes the current state of the switch.

•	No Change - Leaves the switch in its current state.

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Waters 2690/2695 Event Table Operation

To add an event, enter a time, select an event from the drop down list box, select an action and press the [image] toolbar button. Up to 16 events can be programmed.

To delete a single event, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

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Waters 996 PDA Detector

This page is used to set parameters specific to the UV detector, to access it select View, Waters996 PDA Detector, select Detector from the short cut bar or press the [image] toolbar button.

Start Wavelength	Enter the wavelength at which to start acquiring data.
End Wavelength	Enter the wavelength at which to stop acquiring data. The range with Resolution set to 1.2 is 190.0 nm to 800.0 nm. The range at all other Resolution settings is 190.0 + (Resolution/2) to 800.0 (Resolution/2).
Resolution	Enter the number of diodes that are averaged together as a single spectral data point. To differentiate closely related spectra and obtain greater spectral resolution, use a small resolution number. Be aware, however, that a small resolution value generates more data points and therefore requires more disk space than a large resolution value. Find a resolution value just small enough to identify spectral features. Range: 1.2 to 24.0 nm in multiples of 1.2
Sampling Rate	Select the number of Spectra to be acquired per second, from the dropdown list box. For good integration and quantitation, acquire 15 to 20 spectra across a peak.
Auto Exposure	Check this box to enable the detector optics to calculate the optimum exposure time needed to recharge the diodes, based on the lamp energy, the lamp spectrum and the selected wavelength range. Tip: Enable Auto Exposure for most routine analyses.
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Waters 996 PDA Page

Waters 996 Channel Detector Configuration Pages


Waters 996 PDA Page

Interpolate	Check this box to instruct the detector to ignore the signal from the photodiode at 656 nm and interpolate a value from the adjacent diodes. This prevents over-saturation at 656 nm (Balmer line for deuterium). Only applicable if the Auto Exposure option has been selected. If this box is not checked the detector reports the signal from the photodiode at 656 nm, this is only necessary if you are working with compounds that absorb in the 656 nm range. Note: If this parameter is unchecked, the deuterium lamp high emission line at 656 nm may cause spectral artifacts and autoexposure errors.
Exposure Time	The exposure time is the time that the photodiodes are exposed to light before they are read. To set a different Exposure Time, ensure that the Auto Exposure box is not checked and enter the required time in milli seconds.  Range: 11.00 to 500.00 ms.
Stop Time	To specify a different Acquisition Stop Time enter the time in minutes when the PDA should stop scanning.
Filter Response	Enter the response time for filtering acquired data. The filter is an enhanced rolling average filter applied to absorbance data from the PDA detector before the data is sent to MassLynx. The filter reduces high-frequency noise across the entire wavelength range specified for the acquisition. High values decrease peak response. Available choices: 0, 1, 2 and 3.
Save to Disk	Check this box to save the Photo Diode Array data to the raw datafile. If this data is not required for further processing then uncheck the box, the data is not saved to disk thus reducing the size of the file.
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Waters 996 Channel Detector Configuration Pages

The Channel 1 and Channel 2 pages contain the same information. Select the page relevant to the channel required, by clicking on the tab.

Output Mode	Select one of:- • Off - no analog output signal. • Absorbance - Output is in absorbance units at the wavelength specified. Note: Ratio Denominator Wavelength and Threshold parameters are not accessible when Absorbance mode is selected. • Ratio - Output represents the ratio of absorbances at two wavelengths. The numerator wavelength is specified by the Wavelength parameter, and the denominator wavelength is specified by the Ratio Denominator Wavelength parameter (see below).
Wavelength	Enter the output wavelength to monitor. In Ratio mode, the absorbance at the Wavelength is used to calculate ratio in the formula: Ratio = Absorbance at Wavelength/Absorbance at Ratio Denominator Wavelength  Wavelength must be within the wavelength range specified by the Start Wavelength and End Wavelength parameters on the PDA page Range when Resolution is set to 1.2: Start Wavelength to End Wavelength. Range at all other Resolution settings: Start Wavelength + (Bandwidth/2) to End Wavelength - (Bandwidth/2). Default: 254 nm.
Ratio Denominator Wavelength	Enter the denominator wavelength (in nanometers) for the analog output channel. Ratio Denominator Wavelength must be within the wavelength range specified by the Start Wavelength and End Wavelength parameters on the 996 PDA page.
Bandwidth	Enter the spectral bandwidth of the analog output channel. The range is 1.2 to 24.0 nm.
Filter Type	Select Hamming or Single Pole from the dropdown list box. The Hamming filter is designed to create the same degree of peak-height degradation as the Single Pole filter for the same response time, but enhances filtering of high-frequency noise.
Filter Response	Enter the response time for the filter. The range is 0 to 5 seconds.
Offset	If required enter an offset to the analog output channel. The range is -0.2 to 2.0 AU.
Threshold	Enter a threshold above which the ratio (Wavelength / Ratio Denominator Wavelength) must be to be valid data. The range is -0.1 to 2.0 AU. Note: If no ratio is plotted one or both channels are below the current Threshold and a lower Threshold value should be entered.
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Waters 486 UV Detector

This page is used to set parameters specific to the UV detector, to access it select View, Waters486 UV Detector, select Detector from the short cut bar or press the [image] toolbar button.

Wavelength ()	Enter the wavelength to monitor.
Polarity	Select the polarity of the output signal from the drop down list box.
Sensitivity (AUFS)	Enter the required sensitivity of the output signal.
Time Filter (seconds)	Enter the response time for filtering acquired data.
A full description of all the parameters in this editor is given in the Waters 486 Instruction Manual.


Waters 2487 UV Detector

This page is used to set parameters specific to the Waters 2487 UV detector, to access it select View, Waters2487 UV Detector, select Detector from the short cut bar or press the [image] toolbar button.

More:

2487 Single Wavelength Absorbance Detector

2487 Dual Wavelength Absorbance Detector


2487 Single Wavelength Absorbance Detector

The 2487 detector can be used as a single or dual wavelength detector. To use as a single wavelength detector select Single Wavelength from the Waters2487 UV menu. A tick mark will appear next to the name if single wavelength is selected and the 2487 Channel B parameters are grayed out.

Wavelength ()	Enter the wavelength to monitor.
Sensitivity (AUFS)	Enter the required sensitivity of the output signal.
Time Filter (seconds)	Enter the response time for filtering acquired data.
Polarity	Select the polarity of the output signal from the drop down list box.
A full description of all the parameters in this editor is given in the Waters 2487 Instruction Manual.

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2487 Dual Wavelength Absorbance Detector

The 2487 detector can be used as a single or dual wavelength detector. To use as a dual wavelength detector ensure that the Single Wavelength option on the Waters2487UV menu is not selected. If a tick mark appears next to the name then single wavelength is selected, selecting the option again will return the detector to dual wavelength mode and both channel parameters will be available.

The parameters are the same as for single wavelength mode.

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Waters 2487 IEEE Detector

The 2487 IEEE Detector should be selected if the detector is connected via a GPIB card in the back of the PC.

The 2487 IEEE Detector is used to collect binary data, through the IEEE interface, rather than through the analog interface.

Note. Waters control sofware needs to be installed before using this instrument.

This page is used to set parameters specific to the Waters 2487 IEEE detector, to access it select Waters2487 IEEE Detector from the View menu, select Detector from the short cut bar or press the [image] toolbar button..

The 2487 detector can be used as a single or dual wavelength detector. Check Single or Dual under Wavelength Mode

A full description of all the parameters in this editor is given in the Waters 2487 Instruction Manual.

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Waters SAT/IN PDA Detector

This page is used to set parameters specific to the PDA detector, to access it select View, WatersSATIN PDA Detector, select Detector from the short cut bar or press the [image] toolbar button..

Channel 1 and Channel 2	Check the box(es) for the required channels.
Sampling Rate	Select the number of Spectra to be acquired per second, from the dropdown list box. For good integration and quantitation, acquire 15 to 20 spectra across a peak.
Notes

Data collected through a Waters SAT/IN PDA Detector is shown as analog data in the acquired data files, this is the same as analog data coming in through the analog inputs from the back of an MS instrument.

The Waters SAT/IN PDA Detector can be used to collect analog data or the MS analog inputs can be used. Do not try to collect analog data with the SAT/IN and the MS analog inputs at the same time. Collecting analog data from both sources will result in unpredictable behavior.

SAT/IN analog data will only be collected in a system configured with a spectral data source. An MS detector and/or a PDA detector must also be used to successfully collect SAT/IN data.

Negative data is not supported by the Waters SAT/IN but can be avoided by applying an appropriate offset in the connected Detector.


Waters 2700 Autosampler

These pages are used to set parameters specific to the autosampler, to access them select View, Waters2700 AutoSampler, select Autosampler from the short cut bar or press the [image] toolbar button.

More:

Waters 2700 Injection Configuration

Waters 2700 Dilutor Configuration

Waters 2700 Wash Parameters

Waters 2700 Sample Configuration

Waters 2700 Bed Layout

Waters 2700 Fixed Positions

Waters 2700 Plate Generator

Waters 2700 Menu


Waters 2700 Injection Configuration

Injection Type	Select from Full or Partial Loop.
Loop Volume (l)	Enter the volume of the sample loop in microlitres
Injection Volume (l)	Only enabled for Partial Loop. Enter the volume of the sample to inject into the loop for single sample acquisitions. For samples acquired via a sample list this is overridden by the value in the sample list. If the Injection Volume is equal to the Loop Volume then twice the Injection Volume is drawn to ensure that the loop is full.
Separation Air Gap (l)	Enter the volume of air to draw before the sample.
Loop Overfill	Enabled only for Full Loop inject mode.
Vial Reference	Enter the position of the vial to use for single sample acquisitions. For samples acquired via a sample list this is overridden by the value in the sample list.
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Waters 2700 Dilutor Configuration

Syringe Size	Select the size of the syringe installed from the drop down list box.
Aspiration Speed	Enter a value for the speed at which to draw the sample into the needle (the pump will be on its downward journey). Range: 1 to 32, with 1 being the fastest.
Dispense Speed	Enter a value for the speed at which to eject the sample from the needle (the pump will be on its upward journey). Range: 1 to 32, with 1 being the fastest.
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Waters 2700 Wash Parameters

Needle Rinse Volume (l)	Enter the volume of mobile phase required to wash the needle after an injection. A value of zero will result in no wash. If the needle rinse volume is greater than 800l then the mini-wash pump is used instead.
Wash Time (seconds)	Enter the time for which the mini-wash pump is activated during a mini-wash prime. Mini-wash prime is activated from the Waters2700 menu.
Injection Port Flush Volume (l)	Enter the volume of mobile phase required to flush the inject port after the sample has been injected. A value of zero will result in no port flush.
Injection Port Flush Speed	Enter the speed at which the flush volume is dispensed. Range: 1 to 32, with 1 being the fastest.
 Related Topics


Waters 2700 Sample Configuration

Current Layout	This shows the currently selected rack configuration. To change the current layout select a new one from the drop down list box.
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Waters 2700 Bed Layout

Bed layouts are created, deleted or amended from this dialog. To display the Bed Layout Editor dialog, select Waters2700, Bed Layout.

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To Create A New Bed Layout (Waters 2700

To Delete A Bed Layout (Waters 2700

Other Bed Layout Options (Waters 2700

Modify Bed Layout (Waters 2700


To Create A New Bed Layout (Waters 2700

1.	Highlight a bed layout similar to the one you want to create and press the [image] button to create a new layout. The layout appears in the Bed Layouts list as the same name with a 1 at the end, e.g. Six Position Microtiter1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

New bed layouts are saved to the MassLynx Racks directory.

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To Delete A Bed Layout (Waters 2700

1.	Highlight the bed layout to delete and press the [image] button. A dialog box will ask you to confirm the deletion. Press the OK button to delete the bed layout. Note: The bed layout which is selected as the current bed layout on the Sampler Configuration page cannot be deleted.

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Other Bed Layout Options (Waters 2700

2.	To change the number of rows in the current column, type the new number into the Rows box and press the [image] button.

3.	To append a new column, press the [image] button.

4.	To delete the current column press the [image] button.

5.	To insert a column, click on the column before which you want to insert and press the [image] button. Note: The column inserted will have the same number of rows as the column highlighted.

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Modify Bed Layout (Waters 2700

If the plate position or type needs changing select the Modify Bed Layout tab.

Click on one of the code plates to display the Plate Position and Type dialog.

This dialog allows you to select a new plate from a list of possible options, and change its actual position on the bed. Measurements for plate positions are always taken from the top left corner of each plate. The X value is the measurement from the vial position in the top left corner of the plate to the home position. The Y value is the measurement from the vial position in the top left corner of the plate to the home position.

Vial bottom from probe home	This is the distance the needle must travel downwards to reach the bottom of the well.
OpenLynx plate login	If this box is checked and Use current MassLynx autosampler bed layout is checked in the OpenLynx Manager program, then the plate at this position can only be used for plate login on the OpenLynx Login program.
Pressing the [image] button will move the needle to the top left vial position defined by the X, Y and Vial bottom from probe home positions. If the needle is not above the top left vial then the plate will need moving or the X and Y values will need changing.

Pressing the [image] button will take the needle to the bottom right vial position (The software will calculate this from the plate type and the X and Y positions defined). This is used to test that the plate will fit on the autosampler, if it does not then an error message is displayed. The plate will need changing or moving or the X and Y values will need changing.

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Waters 2700 Fixed Positions

This dialog allows the positions of the Injector Port, Cleaner Stations and the Waste station to be defined. It is accessed by selecting Waters2700, Edit Fixed Positions.

The X and Y values are the distance the needle must travel from the Home position to the required station.

The Z value is the distance the needle must travel downwards to reach the required station.

To test that the values entered are valid press the [image] button. The needle will travel to the position specified. To return the needle to the Home position, press the [image] button.

When all values are correct press the OK button.

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Waters 2700 Plate Generator

To display the Plate Generator dialog, select Plate Generator from the Waters2700 menu.

Plate Name	The name of the plate that is currently being edited.
Rows	The number of vials in a row and the distance between each center.
Columns	The number of vials in a column and the distance between each center.
Offsets	Allows alternate vial rows or columns to be offset.  Note: Entering a positive value will shift even numbered rows to the right and negative values will shift even numbered rows to the left.
Vial Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Referencing	This has three options  • XY which references the vials A1, B1 etc. • Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to right, then continues number the next row, right to left etc. If the Waters 2700 autosampler is used with OpenLynx then the vial referencing must be set to either sequential continuous or sequential discontinuous.
Priority	Check the Horizontal First box if samples are to be acquired horizontally across the plate. If Referencing = X,Y, Horizontal = Letter, Vertical = Number and Horizontal Priority is checked, this will result in samples being acquired in the order A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired in the order 1A, 1B, 1C etc. If Referencing = sequential continuous or discontinuous and Horizontal Priority is checked, this will result in samples being acquired from row 1 then row 2. If the Horizontal Priority box is not checked samples will be acquired from column 1 then column 2 etc.
Plate Size	The size of the plate to its outside edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate
Vial	The depth and diameter values are used for display only. They appear in the description for a single shot login on the OpenLynx Login screen.
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Creating and Deleting Waters 2700 Plates


Creating and Deleting Waters 2700 Plates

To create a new plate, press the [image] button. A new default plate is displayed, change the Plate Name, enter the appropriate values and press the save [image] button or select Save Plate from the Plate menu. New plates are saved to the MassLynx Plates directory.

To copy a plate, page through the list of saved plates using the [image] and [image] toolbar buttons.  The Previous Plate and Next Plate options on the Plate menu perform the same operation. When the required plate is displayed change the Plate Name, enter the appropriate values and press the save [image] button or select Save Plate from the Plate menu. New plates are saved to the MassLynx Plates directory.

To delete a plate select the plate, by typing the name in the Plate Name box or by paging through as above, and press the delete [image] button or choose Delete Plate from the Plate menu.

Note: All of the spacings and the vial section are stored in 0.1mm units.

Note: When defining a custom plate for use with a multi-injector the plate is required to be compatible with the position of the 8 needles of the autosampler.

•	The Plate must have eight columns.

•	The position of the vials should allow all eight needles to enter a separate vial.

•	There should be no odd or even offsets for any of the vial positions.

Note: If the Plate currently selected on the Sample Configuration page is changed here, then Reset Injector should be selected from the LC menu to reset communications.

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Waters 2700 Menu

Prime Syringe	This option is used to remove air from the syringe and any tubing connected to it. It repeatedly draws the mobile phase into the needle and flushes it out until the [image] toolbar button is pressed, or Stop Method is selected from the LC menu, on the Inlet Editor. Note: Before Prime Syringe is selected the toolbar button appears as [image] and the menu as Run Method.
Change Syringe	Selecting this option moves the needle to a position where it can be removed and replaced. When the syringe has been changed, Prime Syringe should then be selected to get the needle into a state ready for injection.
Prime Mini-Wash	This option moves the needle to the waste position and pumps the mobile phase through it for the Wash Time defined on the Wash Parameters page.
 Related Topics


Waters 2790/2795 Autosampler

Note: To control the Waters 2790/2795 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None. See Configuring the Inlet System in the Acquisition Control Panel chapter.

These pages are used to set parameters specific to the Sampler, to access them select View, Waters2790/2795 AutoSampler, select Autosampler from the short cut bar or press the [image] toolbar button.

More:

Waters 2790/2795 Injection Parameters Page

Waters 2790/2795 Autosampler Parameters Page

Waters 2790/2795 Wash Parameters Page


Waters 2790/2795 Injection Parameters Page

Inject Type	Select Sequential or Parallel from the drop down list box. Sequential - Sample aspiration occurs at the start of each injection cycle, after completion of the previous injection. Parallel - Sample aspiration and loop fill occur concurrently with other separation method functions for higher throughput.
Fill Mode	Select Full Loop or Partial Loop from the drop down list box. Full Loop - The autosampler draws in the loop volume the overfill factor number of times, to ensure that the loop is full. Partial Loop - The autosampler will draw in the volume specified in the sample list and center it in the loop.
Aspirate Air Pre-sample	Enter the volume of air to be drawn into the needle before the sample, to separate it from the previous sample. Range: 0 to half the loop size.
Aspirate Air Post-sample	Enter the volume of air to be drawn into the needle after the sample, to separate it from the next sample. Range: 0 to half the loop size.
Loop Off-line Time	For Parallel Injection mode, enter the time in minutes when the injector valve is switched back from the inject position to the load position for the next sample to be preloaded into the sample loop. Range 0.00 to the Run Time defined on the Pump Mobile Phase page, in minutes.
Overfill Factor	For full loop mode enter the number of times to draw the loop volume into the loop to ensure that it is full. Range 1.0 to 20.
 Related Topics


Waters 2790/2795 Autosampler Parameters Page

Sample Temperature Set	If the sample heater is installed, enter the temperature to heat or cool the sample to. Range: 4.0 to 40.0 C.
Sample Temperature Limit	This is the maximum deviation in sample temperature allowed. If this is exceeded the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red. Range: ±1.0 to ±20.0 C.
Loop Size (l)	This is a display only field showing the volume of the sample loop installed.
Syringe Size	This is a display only field showing the size of the syringe installed.
Draw Depth	Adjusts the depth of the needle tip to accommodate for sedimented samples or non-standard vials. A value of 0 corresponds to the bottom of the vial. Range: 0.0 to 20.0 mm.
Draw Speed	This determines the rate in microlitres per second at which sample is extracted into the autosampler needle. This should be set according to the viscosity of the sample. Select one of Fast, Normal or Slow from the dropdown list box. The table below shows the draw rate for each selection using a 250 l syringe.
Selection	Draw Rate for a 250 l Syringe
Fast	5.0 l/sec
Normal	2.5 l/sec
Slow	1.0 l/sec
Custom	Value entered in the Custom Speed box.
Seek Well Bottom	If this box is checked then, for the first well on a plate, the needle will automatically seek the bottom of the well before drawing the sample. The depth of the well will be saved by the software and used as the depth for all other wells on the plate. This will be repeated for the first well on each plate. Note: If a value has been entered in the Draw Depth field then this operation will not be performed.
Check Plate Height	If this box is checked, for the first injection from a plate, a needle positioning sensor determines the plate height then checks it against the Plate Size, Z value defined in the Plate Generator.
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Waters 2790/2795 Wash Parameters Page

Wash Frequency	Select the wash frequency from the drop down list box. • None Do not perform a wash. • Inject Perform a wash after each injection. • Well Perform a wash after all samples have been taken from the current well.
Inject Port	Enter the time in seconds to wash the interior of the needle for.
Needle Exterior	Enter the time in seconds to wash the exterior of the needle for. Range: 0 to 99 seconds.
Wash Cycles	Enter the number of times the Inject Port and Needle Exterior washes are to be performed. Range: 0 to 10.
Replacement Volume	Enter the volume of wash solvent to leave in the needle after the wash/flush operation has been performed. This volume is then drawn through the waste valve and dispensed into the sample line through the needle. Range: 0 to 9999 ìl.
Wash Sequence	Choose from Wash - Purge or Purge- Wash - Purge
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Waters 2790/2795 Pump

Note: To control the Waters 2790/2795 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None

The Waters Pump pages can be accessed by selecting View, Waters2790/2795 Pump from the menu on the Inlet Editor, selecting Inlet from the short cut bar or by pressing the [image] toolbar button.

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must equal 100%. Solvent Names entered here will be displayed on the Gradient page.
Pump A	This displays the remainder percentage after the solvent percentages have been set for the other enabled pumps.
Pump B, C and D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Flow	Enter the total initial flow rate of the system. Range: 0.000 to 10.000 ml/min.
Ramp	Enter the time (in minutes) for the solvent delivery system to reach the maximum system flow rate (10 ml/min). This limits the rate of change of the flow rate to protect the column from potentially damaging sudden changes in pressure. Range: 0.01 to 30 minutes. Recommended minimum setting: 0.5 min.
 Related Topics

More:

Waters 2790/2795 Mobile Phase Page

Waters 2790/2795 Column Page

Waters 2790/2795 Rapid Equilibration Page

Waters 2790/2795 I/O Page

Waters 2790/2795 Gradient Page

Waters 2790/2795 Events Page

Waters 2790/2795 Method Type Page

Waters 2790/2795 Menu

Waters 2790/2795 Plate Generator

Waters 2790/2795 Bed Layout


Waters 2790/2795 Mobile Phase Page

Low Pressure Limit and High Pressure Limit	Enter values as required. If the pressure falls outside these limits the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red. Low Pressure Range: 0 to 310 bar. High Pressure Range: 0 to 345 bar.
Degasser	Select one of Off, Normal or Continuous from the drop down list box. • Off The degasser is always off. • Normal The degasser cycles on and off. • Continuous The degasser is always on.
Stroke Length	This sets the volume of solvent delivered for each piston stroke. Select the required option from the drop down list box. If Auto is selected then the volume is automatically adjusted to provide optimal performance for the selected solvent flow rate, otherwise the volume selected will be used.
Run Time	Enter the time in minutes that the method will run from the point of injection. Note: Run time is for the solvent delivery system only. Detectors have independent run times. The MS method (Scan Function Editor) run time must be greater than all other run times.
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Waters 2790/2795 Column Page

Position	This field allows the column to be selected for the method. The options available will depend on the column setup on the Waters 2790/2795 Separations Module. If only one column is installed then this box will display Column 1 and cannot be changed. For other configurations this box will allow the selection of a column (between 1 and 6 depending on configuration) or No change from the drop down list box. Selecting a numbered column will use this column for the method, selecting No Change will use the column defined in the last method used to acquire a sample. See the Waters 2790/2795 Separations Module Operator's Guide for more information on the column selection valve.
Equilibrium Time	Enter the time required to reach equilibrium (i.e. run in initial conditions), before performing an injection, after a column change. Range: 0.00 to 999.99 minutes.
Temperature Set	Enter the target operating temperature for the optional column heater. This value must be at least 5 C above ambient. Range: 20 to 60 C.
Temperature Limit	Enter the maximum deviation in column temperature allowed. If this is exceeded the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red. Range: ±1 to ±20 C.
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Waters 2790/2795 Rapid Equilibration Page

Path	Select the path to be used for flushing solvent during rapid equilibration from the drop down list box. Waste, Off or Column 1 to Column 6 depending on the instrument configuration.
Flow	Enter the system equilibration flow rate. Range: 0.00 to 10.00 ml/min.
Time	Enter the length of time (in minutes) to equilibrate. Range 0.00 to 999.99 minutes.
Re-equilibration Time	Enter the time that column should be maintained at initial flow/composition conditions after completion of a gradient run. This delay is imposed on a per injection basis if defined.
Pre-column Volume	Enter the volume of solvent to pump through the column between the time the gradient starts and the time of injection. Range: 0.0 to 10000.0 µl
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Waters 2790/2795 I/O Page

Switch Initial Conditions	Select the state that switches 1 to 4 should be in initially, from the drop down list box. At the beginning of each injection cycle each switch returns to the state defined here. Available choices: • On - Turns on a contact closure that triggers an external or internal event. With this function, the contact closure remains closed until an Off function is sent. • Off - Turns off the contact closure for the event. With this function, the contact closure is broken. • Pulse - Transmits a single On/Off pulse. The contact closure is maintained for the number of minutes set in the Pulse Width field on the Events page. Range: 0.01 to 100.00 sec. • Toggle - Changes the current state of the switch. • No Change - Leaves the switch in its current state.
Chart Output Setting	Select Flow Rate, System Pressure, %A, %B, %C, %D, Column Temperature or Sample Temperature from the drop down list box. The Analog output signals are sent through the terminals on the back of the 2790/2795, to an optional analog device such as a strip chart recorder. If, for example, System Pressure is selected the recorder will chart the system pressure while the method is being run.
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Waters 2790/2795 Gradient Page

This page allows a gradient to be entered and edited. If you wish to operate in isocratic mode then enter parameters on the Mobile Phase page and ensure that the timetable is empty.

Time (mins)	Specifies the time at which the specified conditions (%A to %D, Flow, and Curve) for the row should take effect. Make sure the Time for the first row is set to 0.00, to establish initial conditions for the gradient run. The range for rows other than row 1is 0.01 to 999.99 minutes.
Solvent A % - Solvent D%	Specifies the percentage of solvent flow from each reservoir. For each row the total of all solvents must equal 100%. Range: 0 to 100%.
Flow (ml/min)	Specifies the total flow rate for the solvent delivery system. Range: 1 to 10 ml/min. Note: If column equilibration, rapid equilibration or wet prime are performed then the flow rate will return to the value defined on the Mobile Phase page. If they are not performed then the flow rate will stay at the value defined for the last entry in the Gradient Table. To return to the initial flow rate an entry must be added to the end of the table setting the value to that defined on the Mobile Phase page.
Curve	This sets the rate at which the solvent is to change to the new proportions and/or flow rates. Curves are specified by number. Available choices: 1 to 11.(see also Waters 2690/2695 Pump Gradient Page)
Curve Number	Effect
1	Immediately goes to specified conditions
2 to 5	Convex
6	Linear
7 to 10	Concave
11	Maintains start condition until next step
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Waters 2790/2795 Gradient Table Operation


Waters 2790/2795 Gradient Table Operation

To add a gradient, enter values in the relevant boxes and press the [image] toolbar button. Up to 15 rows can be added to the table. Note: The first entry must have a time of 0.

To delete a single gradient click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being.

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Waters 2790/2795 Events Page

Use the Event Table to program up to 16 events (both external and internal). The external events are triggered by four contact closures (relays) through output terminals (S1-S4) on the 2790/2795 Separations Module. The internal events are used to control the sample compartment temperature, column heater temperature and column change. Events can be triggered more than once and multiple events can be triggered simultaneously.

Time	Enter the time at which the event starts. Event rows are sorted automatically by time. Note: Different events can be programmed to occur at the same time. Range 0.00 to the Run Time defined on the Mobile Phase page, in minutes.
Event	Enter the type of event signal: one of the four TTL-level output switches (S1-S4), or one of the internal events (column heater temperature, sample compartment or column change). • Switch 1 to Switch 4 Corresponds to terminal strip positions S1 to S4 on the rear of the 2790/2795 module. Activating a Switch event triggers a contact closure for controlling an external device. After selecting a switch event, set a state for the switch by selecting On, Off, Toggle, Pulse Width or No Change. This state appears in the Action column of the table (see Switch States, below). Note: If Pulse is selected the duration of the pulse must be entered in the Width (min) field. • Set Temperature (Column or Sample) Specifies the temperature of an optional column heater, or an optional sample compartment heater/cooler. After selecting this event, select Column or Sample and enter the required Temperature in C. Note: When a Column Temperature event occurs, the temperature of the column heater changes from the value set in the Column page to the value set for the event. When the event times out, the temperature changes back to the Column page value. Column range: 20 to 60 C. Sample range: 4 to 40 C. • Column Change Specifies a column change operation for the 2790/2795 module, as describe on the Column page.
Switch States	• On - Turns on a contact closure that triggers an external or internal event. With this function, the contact closure remains closed until an Off function is sent. • Off - Turns off the contact closure for the event. With this function, the contact closure is broken. • Toggle - Changes the current state of the switch. • Pulse - Transmits a single On/Off pulse. The contact closure is maintained for the number of seconds that defined in the Value column. Range: 0.01 to 10.00 sec. • No Change - Leaves the switch in its current state.
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Waters 2790/2795 Event Table Operation


Waters 2790/2795 Event Table Operation

To add an event, type in a time, select an event from the drop down list box, select an action and press the [image] toolbar button. Up to 16 events can be programmed.

To delete a single event click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry.

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Waters 2790/2795 Method Type Page

This page is used for creating normal, pre and post run methods. First create a Normal method and save the file, then create any pre or post run methods (saving them under different names). These methods can then be defined in the Inlet Prerun and Inlet Postrun columns of the Sample List.

Method Type	Select the type of method to create. The Parameters section will be updated to show the parameters required for the selected method.
Normal	Creates a normal method. No extra parameters need to be defined.
For all other method types see the Waters 2790/2795 Menu for details of the parameters required.

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Waters 2790/2795 Menu

Waters 2790/2795 Wet Prime

Waters 2790/2795 Equilibrate

Waters 2790/2795 Condition Column

Waters 2790/2795 Wash Needle

Waters 2790/2795 Refresh Syringe


Waters 2790/2795 Wet Prime

Wet Prime	A wet prime should be performed when changing the solvent in the system to flush out the previous solvent. The new solvent is pumped through the tubing and the Prime port of the Inject valve to waste. Enter the Flow rate, Time and the Percentage of solvents to use then press the Prime button. Waters recommend that the wet prime is started using the solvent with the lowest viscosity to help purge air from the lines, especially if the in-line vacuum degasser is installed.
Note: If the solvent lines are dry then a dry prime must be performed before a wet prime. See the Waters 2790/2795 Separation Module Operator's Guide for more information on performing a dry prime.

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Waters 2790/2795 Equilibrate

Equilibrate	Equilibrates the system using the parameters defined on the Mobile Phase page. Enter the Time to equilibrate the system for and press OK. The time needed to equilibrate the system will depend on environmental and application-specific factors.
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Waters 2790/2795 Condition Column

Condition Column	Runs solvent through the column without injecting samples or running the Events table. Solvent is delivered to the Column defined on the Column page, using the Gradient Table defined on the Gradient page. Enter the Time in minutes to condition the column for and press OK. Ensure that the time is equal to or greater than the Time of the last entry in the Gradient Table (defined on the Gradient page) plus the Re-equilibration Time (defined on the Rapid Equilibration page).
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Waters 2790/2795 Wash Needle

Wash Needle	Washes the inject port, and both the interior and exterior of the needle with wash solvent, and then fills the needle with fresh solvent. Enter the number of wash Cycles to perform and the Volume of wash solvent to use then press OK. Waters recommend a volume of 600 μl.
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Waters 2790/2795 Refresh Syringe

Refresh Syringe refills the syringe with fresh, degassed, purge solvent.

Enter the number of Cycles and the replacement Volume and press OK. Waters recommend 12 Cycles and a volume of 600 μl.

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Waters 2790/2795 Plate Generator

To display the Plate Generator dialog, select Plate Generator from the Waters2790/2795 menu.

Plate Name	The name of the plate that is currently being edited.
Rows	The number of vials in a row and the distance between each center.
Columns	The number of vials in a column and the distance between each center.
Offsets	Allows alternate vial rows or columns to be offset. Note: Entering a positive value will shift even numbered rows to the right and negative values will shift even numbered rows to the left.
Vial Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Horizontal	Sets the horizontal axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing.
Vertical	Sets the vertical axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing.
Referencing	This has three options  • XY which references the vials A1, B1 etc. • Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to right, then continues number the next row, right to left etc. If the Waters 2790/2795 autosampler is used with OpenLynx then the vial referencing must be set to either sequential continuous or sequential discontinuous.
Priority	Check the Horizontal First box if samples are to be acquired horizontally across the plate. If Referencing = X,Y, Horizontal = Letter, Vertical = Number and Horizontal Priority is checked, this will result in samples being acquired in the order A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired in the order 1A, 1B, 1C etc. If Referencing = sequential continuous or discontinuous and Horizontal Priority is checked, this will result in samples being acquired from row 1 then row 2. If the Horizontal Priority box is not checked samples will be acquired from column 1, then column 2 etc.
Plate Size	The size of the plate to its outside edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate.
Vial	The depth and diameter values are used for display only. They appear in the description for a single shot login on the OpenLynx Login screen.
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Creating and Deleting Waters 2790/2795 Plates

Vial Referencing Examples


Creating and Deleting Waters 2790/2795 Plates

To create a new plate, press the [image] button. A new default plate is displayed, change the Plate Name, enter the appropriate values and press the save [image] button or select Plate, Save Plate. New plates are saved to the MassLynx Plates directory.

To copy a plate, page through the list of saved plates using the [image] and [image] toolbar buttons.  The Previous Plate and Next Plate options on the Plate menu perform the same operation. When the required plate is displayed change the Plate Name, enter the appropriate values and press the save [image] button or select Plate, Save Plate. New plates are saved to the MassLynx Plates directory.

To delete a plate select the plate, by typing the name in the Plate Name box or by paging through as above, and press the delete [image] button or choose Plate, Delete Plate .

Note: All of the spacings and the vial section are stored in 0.1 mm units.

Note: When defining a custom plate for use with a multi-injector the plate is required to be compatible with the position of the 8 needles of the autosampler.

•	The Plate must have eight columns.

•	The position of the vials should allow all eight needles to enter a separate vial.

•	There should be no odd or even offsets for any of the vial positions.

Note: If the Plate currently selected on the Sample Configuration page is changed here, then Reset Injector should be selected from the LC menu to reset communications.

Note: All of the spacings and the vial section are stored in 0.1 mm units.

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Waters Systems - Waters 2790/2795 Plate Generator - Vial Referencing Examples
Vial Referencing Examples

The following tables show four examples of vial referencing for a simplified 4 × 3 vial plate.

	1	2	3	4	Horizontal: 123
A	1,A	2,A	3,A	4,A	Vertical: ABC
B	1,B	2,B	3,B	4,B	Referencing: XY
C	1,C	2,C	3,C	4,C	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: 123
A	A,1	A,2	A,3	A,4	Vertical: ABC
B	B,1	B,2	B,3	B,4	Referencing: XY
C	C,1	C,2	C,3	C,4	Priority: Horizontal First NOT Checked
	1	2	3	4	Horizontal: N/A
A	1	2	3	4	Vertical: N/A
B	5	6	7	8	Referencing: Sequential Discontinuous
C	9	10	11	12	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: N/A
A	1	6	7	12	Vertical: N/A
B	2	5	8	11	Referencing: Sequential Continuous
C	3	4	9	10	Priority: Horizontal First NOT Checked
 Related Topics


Waters 2790/2795 Bed Layout

Use the Bed Layout Editor to define the type, number, and location of the well plates on the 2790/2795 plate carrier. To access the Bed Layout Editor, select Bed Layout from the Waters2790/2795 menu.

Bed Layouts	Lists the available Bed Layouts.
Current Layout	Specifies the bed layout currently in use.
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More:

To Delete A Bed Layout (Waters 2790/2795

To Create A New Bed Layout (Waters 2790/2795

To Modify a Bed Layout (Waters 2790/2795)


To Delete A Bed Layout (Waters 2790/2795

1.	Highlight the bed layout to delete and press the [image] button. A dialog box will ask you to confirm the deletion. Press the OK button to delete the bed layout.

Note: You cannot delete the bed layout which is selected as the Current Layout.

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To Create A New Bed Layout (Waters 2790/2795

1.	Highlight a bed layout similar to the one you want to create and press the [image] button to create a new layout. The layout appears in the Bed Layouts list as the same name with a 1 at the end, for example Six Position Microtiter1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

3.	If the plate position or type needs changing select the Modify Bed Layout tab.

Note: New bed layouts are saved to the MassLynx Racks directory.

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To Modify a Bed Layout (Waters 2790/2795)

Use the Modify Bed Layout page to modify an existing bed layout. To access the Modify Bed Layout page, click the Modify Bed Layout tab. The Modify Bed Layout page shows a graphical representation of the selected bed layout. There are four plate positions in the 2790/2795.

Click the plate that you want to change to display the Plate Position and Type dialog.

This dialog allows you to select a new plate from a list of possible options, and change its actual position on the bed. Select the plate type you want to use in the bed layout, then click OK.

OpenLynx plate login	If this box is checked and Use current MassLynx autosampler bed layout is checked in the OpenLynx Manager program, then the plate at this position can only be used for plate login on the OpenLynx Login program.
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Waters 2796 Status Pages

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Waters 2796 Status

Waters 2796 First Dimension / 2796 Page

Waters 2796 / 1525 Page

Waters 2796 Second Dimension Page


Waters 2796 Status

Note: 	Note: To control the Waters 2796 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None.

The Waters 2796 Status pages can be accessed by selecting View, Status from the menu on the Inlet Editor, selecting Status from the shortcut bar, or by pressing the [image] toolbar button.

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Waters 2796 First Dimension / 2796 Page

This page displays the current status of the 2796 Bioseparations Module. (The items on this page are for display purposes only and cannot be edited.)

Indicators	The Running, Pump On, and Injector Cycle indicators show the current status of the 2796. The Ready and OK indicators turn red if the 2796 has an error. You can then click on the red indicators to give you more information on the cause of the malfunction.
Run Time	Displays the run time of the method currently running on the 2796.
Flow Rate	Displays the current flow rate of the 2796.
Pressure	Displays the current system pressure of the 2796.
Column Left and Column Right	Displays the current temperature of the first and second column heaters or heater/coolers. These items will be disabled if the optional column heaters or heater/coolers are not installed.
Sample Temp	Displays the current temperature of the sample heater/cooler. This item will be disabled if the optional sample heater/cooler is not installed.
Gradient	Displays the current solvent composition of the 2796.
PDA Detector	Displays the current detector mode and the number of scans (data points) acquired.
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Waters 2796 / 1525 Page

(Single Dimension / Custom Two Dimension Methods Only)

This page displays the current status of the 1525 pump. (The items on this page are for display purposes only and cannot be edited.)

Indicators	The Pump On indicator shows the current status of the 1525. The Ready and OK indicators turn red if the 1525 has an error. You can then click on the red indicators to give you more information on the cause of the malfunction.
Flow Rate	Displays the current flow rate of the 1525.
Pressure	Displays the current pressure of the 1525.
Gradient	Displays the current composition of the 1525.


Waters 2796 Second Dimension Page

(Comprehensive Two Dimension Step / Sampling Methods Only)

This page displays the current status of the 1525 pump. (The items on this page are for display purposes only and cannot be edited.)

Indicators	The Running and Pump On indicators show the current status of the 1525. The Ready and OK indicators turn red if the 1525 has an error. You can then click on the red indicators to give you more information on the cause of the malfunction.
First Dimension Step	Displays the current step of the first dimension gradient.
Second Dimension ID	Displays the ID of the current second dimension gradient.
Run Time	Displays the run time of the method currently running on the 1525.
Flow Rate	Displays the current flow rate of the 1525.
Pressure	Displays the current pressure of the 1525.
Gradient	Displays the current solvent composition of the 1525.
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Waters 2796 Pump

Note: 	Note: To control the Waters 2796 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None.

The Waters 2796 Pump pages can be accessed by selecting View, Waters 2796Pump from the menu on the Inlet Editor, selecting Inlet from the shortcut bar, or by pressing the [image] toolbar button.

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More:

Waters 2796 Mobile Phase Page

Waters 2796 Column Page

Waters 2796 Rapid Equil Page

Waters 2796 I/O Page

Waters 2796 Events Page

Waters 2796 Method Type Page

Waters 2796 Note Page

Waters 2796 / 1D Sampling Gradient Gradient Page

Waters  2796 1D Gradient Page

Waters 2796 2D-X / 1525 Page


Waters 2796 Mobile Phase Page

Solvent Names	Enter the names of solvents A, B, C, and D (19 characters maximum).
Pressures High Limit / Low Limit	Enter the minimum and maximum pressure limits. If the pressure exceeds these limits the current acquisition will stop and the LC Status OK indicator, on the MassLynx screen, will turn red. Range: 0 to 5000 psi. (A value of 0 disables high or low pressure limit checking.)
Run Time	Enter the run time of the method, from the point of injection. Range: 0 to 999.99 minutes. Note:  Note: This is a display only field in Comprehensive Two Dimension Step / Sampling methods.
Degasser	Select Off or On from the drop down list box.
Stroke Length	Select 25, 50, 100, or 130µL from the drop down list box. This volume is then delivered on each piston stroke. The maximum flow rate for each stroke length is as follows:
	Stroke Length	Maximum Flow Rate
	25 µL	0.53 mL/min
	50 µL	1.23 mL/min
	100 µL	3.03 mL/min
	130 µL	10 mL/min
Time to reach 10mL/min	Enter the amount of time the solvent delivery system should take to reach the maximum system flow rate (10 mL/min). This limits the rate of change of the flow rate to protect the column from potentially damaging sudden changes in pressure. Range: 0.01 to 30 minutes. Recommended minimum setting: 0.5 minutes.
The following  fields are only available if the method is configured with the 1525 enabled.

1525 Solvent Names	Enter the names of solvents E and F (18 characters maximum).
1525 Pressures High Limit / Low Limit	Enter the minimum and maximum pressure limits for the 1525. If the pressure exceeds these limits the current acquisition will stop and the LC Status OK indicator, on the MassLynx screen, will turn red. Range: 0 to 5000 psi.
The following  fields are only available in Comprehensive Two Dimension Step / Sampling methods.

Sampling Steps	This is a display only field showing the total number of sampling steps.
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Waters 2796 Column Page

Position	Select the initial column to use with the method. The columns listed in the drop down list box will depend on the column configuration of the 2796. • Column 1 to Column 6 - Use the specified column. • No Change - Use the current column. Note:  Note: If only one column is configured on the 2796 the drop down list box will be disabled, and Column 1 will be automatically selected.
Equilibration Time	Enter the time required to reach equilibrium (i.e. run in initial conditions), before performing an injection, after a column change. Range: 0 to 999.99 minutes.
Temperature Set	Enter the target operating temperature for the column heater or heater/cooler. This value must be at least 5 °C above ambient for the column heater. Range: 4 to 65 °C.
Temperature Limit	Enter the maximum deviation in column temperature allowed. If this limit is exceeded the current acquisition will stop and the LC Status OK indicator, on the MassLynx screen, will turn red. Range: ±1 to ±20 °C.


Waters 2796 Rapid Equil Page

(Single Dimension / Custom Two Dimension Methods Only)

Path	Select the path to be used for flushing solvent during rapid equilibration from the drop down list box. Waste, Off, or Column 1 to Column 6, depending on the instrument configuration. Selecting Off disables rapid equilibration.
Flow	Enter the rapid equilibration flow rate. Range: 0 to 10 mL/min.
Time	Enter the length of time to equilibrate. Range: 0 to 999.99 minutes.
Re-equilibration Time	Enter the amount of time that the column should be maintained at initial flow/composition conditions after completion of a gradient run. This delay is imposed on a per injection basis if defined. Range: 0 to 999.99 minutes.
Pre-column Volume	Enter the volume of solvent to pump through the column between the time the gradient starts and the time of injection. Range: 0.0 to 10000.0 µL.
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Waters 2796 I/O Page

Switch Initial Conditions	Select the state that switches 1 to 4 should be in initially, from the drop down list boxes. At the beginning of each injection cycle each switch returns to the state defined here. Available choices: • No Change - Leaves the switch in its current state. • On - Turns on the switch by closing the contact closure. • Off - Turns off the switch by opening the contact closure. • Pulse - The switch is turned on (contact closure closed) for 0.01 minutes, then off (contact closure open). • Toggle - Reverses the current state of the switch.
Auxiliary Valve Initial Conditions	Select the position that auxiliary valves 1 to 3 should be in initially, from the drop down list boxes. At the beginning of each injection cycle each valve returns to the position defined here. Available choices: • No Change - Leaves the auxiliary valve in its current position. • Position 1 / Position 2 - Changes the auxiliary valve to the specified position. Note: The auxiliary valves must be enabled in the Peripheral Configuration for these settings to take effect. However, settings for Auxiliary Valves 1 and 2 are always ignored in Comprehensive Two Dimension Step / Sampling methods.
Chart Output Setting	Select Flow Rate, System Pressure, %A, %B, %C, %D, Column Temperature, Sample Temperature, pH, or Conductivity from the drop down list box. The analog output signals are sent through the terminals on the back of the 2796, to an optional analog device such as a strip chart recorder. If, for example, System Pressure is selected the recorder will chart the system pressure while the method is being run.
 Related Topics


Waters 2796 Events Page

Use the Event Table to program up to 16 timed events. Events can be executed more than once, and multiple events can be executed simultaneously.

Time	Enter the time at which to start the event. Events are automatically sorted by time. Range: 0 to 999.99 minutes.
Event	Select the event type from the drop down list box, then specify its parameters: • Switch 1 to Switch 4 - Changes the state of a switch. • On - Turns on the switch by closing the contact closure. • Off - Turns off the switch by opening the contact closure. • Toggle - Reverses the current state of the switch. • Pulse - The switch is turned on (contact closure opens) for the amount of time specified in the Width field, then turned off (contact closure closes). Range: 0.01 to 10 minutes. • No Change - Leaves the switch in its current state. • Set Temperature - Sets the temperature of the column heater or heater/cooler or sample heater/cooler. After selecting this event type, select Column or Sample and enter the required temperature in the Temperature field. Column Temperature Range: 4 to 65 ºC. Sample Temperature Range: 4 to 40 ºC. • Column Change - Selects the column. • Column 1 to Column 6 - Use the specified column. • No Change - Use the current column. • Aux Valve 1 to Aux Valve 3 - Changes the position of an auxiliary valve. Note: Only Aux Valve 3 is available in Comprehensive Two Dimension Step / Sampling methods. • No Change - Leaves the auxiliary valve in its current position. • Position 1 / Position 2 - Changes the auxiliary valve to the specified position. Note: The auxiliary valves must be enabled in the Peripheral Configuration for these settings to take effect. However, settings for Auxiliary Valves 1 and 2 are always ignored in Comprehensive Two Dimension Step / Sampling methods.
More:

Waters 2796 Event Table Operation


Waters 2796 Event Table Operation

Adding a Timed Event

2.	Enter a time, select the event type and enter its parameters, then press the  [image]  toolbar button.

Deleting a Single Timed Event

3.	 Click a time in the list and then press the  [image]  toolbar button.

Deleting all of the Timed Events

Press the  [image]  toolbar button. This button is only available when there are events in the table.

Modifying a Timed Event

6.	Click a time in the list to select the required  event in the Event Table. The properties of the event will then be displayed and can be altered as appropriate.

7.	 Once changes are complete press the  [image]  toolbar button to re-enter the event into the Event Table. If, however, the time value is modified such that it does not correspond to any existing entry in the Event Table, pressing  [image]  will result in a new entry.


Waters 2796 Method Type Page

This page is used for selecting the method type: Normal, Wet Prime, Wash Needle, Refresh Syringe, or System Preparation. To create a prerun or postrun method, first create and save a Normal type method, then change its type and save it under a different name  (Normal type methods can also be used for prerun and postrun). The method can then be used in the Inlet Prerun and Inlet Postrun columns of the Sample List.

Method Type	Select the method type, then specify its parameters: • Normal - Creates a normal method. No extra parameters need to be defined. • Wet Prime - Replaces solvent in the path from the reservoirs through the Prime position of the inject valve to waste. Note:  Note: If the solvent lines are dry, perform the dry prime procedure before continuing. See the Waters 2796 Bioseparations Module Operator's Guide for more information on performing a dry prime. • Flow - The flow rate to use for the wet prime. Range: 0.01 to 10 mL/min. • Time - The amount of time to perform the wet prime. Range: 0 to 999.99 minutes. • Solvent A% to Solvent D% - The composition to use for the wet prime. Range: 0 to 100%. • Wash Needle - Washes the inject port and the needle interior and exterior with wash solvent, and then replaces the wash solvent with purge solvent. • Wash Cycles - The number of wash cycles to perform. Range: 1 to 99. • Inject Port - The amount of time to wash the inject port and the needle interior. Range: 0 to 9999 seconds. • Needle Exterior - The amount of time to wash the needle exterior. Range: 0 to 9999 seconds. • Replacement volume of degassed solvent - The amount of purge solvent to use when replacing the wash solvent. Range: 0 to 9999 µL. • Refresh Syringe - Replaces the solvent in the sample management system with fresh purge solvent. • Strokes - The number of syringe strokes to perform. Range: 1 to 99. • Replacement volume of degassed solvent - The amount of purge solvent to use when replacing the sample management solvent. Range: 0 to 9999 µL. • System Preparation - Prepares the 2796 Bioseparations Module for operation by filling the entire liquid line pathway with fresh eluents, or wash and purge solvents, according to the solvent composition of the method. The System Preparation function accomplishes this by performing a Wet Prime on each of the solvent lines used by the method, washes the needle and purges the syringe, and leaves the system at the initial conditions of the method. • Standard - Performs a standard System Preparation. • Solvent Change - Performs a standard System Preparation as well as an additional Wet Prime on each of the solvent lines used by the method, at 7.0 mL/min.
 Related Topics


Waters 2796 Note Page

This page can be used to enter notes that will be saved with the method. Simply type the notes in the text box and save the method (1024 characters maximum). .

 Related Topics


Waters 2796 / 1D Sampling Gradient Gradient Page

(Single Dimension / Custom Two Dimension  / Comprehensive Two Dimension Sampling Methods Only)

Use the Gradient Table to program up to 50 gradient lines.

Time	Enter the time at which the specified conditions (composition, flow rate, and curve) should take effect. Range: 0 to 999.99 minutes. Note:  Note: A gradient line with time 0 is always present in the Gradient Table. This line indicates the initial conditions of the gradient.
Solvent A% to Solvent D%	Specify the solvent composition for the specified time. For each gradient line the solvent composition must sum to 100%. Range: 0 to 100%.
Flow	Specify the flow rate for the specified time. Range: 0 to 10 mL/min.
Curve	Specify the rate at which the composition and flow rate should change to the conditions of the gradient line. Curves are specified by number (see illustration). Range: 1 to 11. • 1 - The specified conditions take effect immediately. • 2 to 5 - Convex • 6 - Linear • 7 to 10 - Concave • 11 - The specified conditions take effect at the start of the next gradient line.

The following  fields are only available in Comprehensive Two Dimension Sampling methods.

Salt Divert Time	The amount of time the salt divert valve (if present) will remain in the waste position, as well as the amount of time the second dimension gradient will remain at initial conditions, after the column switching valve has brought the 1525 inline with a reverse phase column. This procedure is used to remove salt from the reverse phase column. The salt divert time is also used to indicate when FractionLynx should avoid collecting fractions. Range: 0 - 99 minutes.
Sampling Delay Time	The amount of time added to a second dimension gradient time and a salt divert time to indicate the start of the first sampling step. Range: 0 - 99 minutes.
 Related Topics

More:

Waters 2796 Gradient Table Operation


Waters 2796 Gradient Table Operation

Adding Gradient Line

Enter a time, composition, flow rate, and curve type, then press the  [image]  toolbar button.

Deleting a Single Gradient Line

From the Gradient Table, click a time in the list and then press the  [image]  toolbar button.

Deleting all of the Gradient Lines

Press the  [image]  toolbar button. This button is only available when there are lines in the table.

Modifing a Gradient Line

1.	Click the required line in the Gradient Table. The properties of the line will then be displayed and can be altered as appropriate.

2.	Once changes are complete press the  [image]  toolbar button to re-enter the line into the Gradient Table. If, however, the time value is modified such that it does not correspond to any existing entry in the Gradient Table, pressing  [image]  will result in a new entry.


Waters  2796 1D Gradient Page

(Comprehensive Two Dimension Step Methods Only)

Use the 1D Gradient Table to program up to 50 first dimension gradient lines, and to associate each of those lines with second dimension gradients.

Step	Enter the step number. Range: 1 to 50. Note: Unlike the standard 2796 single dimension gradient table, the 1D Gradient Table is based on steps rather than times. Each line in the 1D Gradient Table has a step number, with its corresponding time being either the global Transfer Time, or the sum of the line's Salt Divert Time and associated second dimension gradient's run time, whichever is greater. During each step, the first dimension gradient is run by the 2796 through the first dimension column and a second dimension column. At the same time, the second dimension gradient is run by the 1525 through the other second dimension column, after the salt divert time has elapsed.
Solvent A% to Solvent D%	Enter the solvent composition for the specified step. For each gradient line the solvent composition must sum to 100%. Range: 0 to 100%.
Flow	Enter the flow rate for the specified time. Range: 0 to 10 mL/min.
Salt Divert	Specify the amount of time the salt divert valve (if present) will remain in the waste position, as well as the amount of time the second dimension gradient will remain at initial conditions, after the column switching valve has brought the 1525 inline with a reverse phase column. The salt divert time is also used to indicate when FractionLynx should avoid collecting fractions. Range: 0 to 99.99 minutes.
2D Table	Specify the second dimension gradient associated with the first dimension gradient line. Range: 2D-1 to 2D-20.
Info	Enter notes related to the gradient line (17 characters maximum).
Flow Curve	Select the global flow curve type. • Step - Indicates that the flow will be changed at the beginning of the step (corresponds to conventional curve type 1). • Linear - Indicates that the flow will change linearly during the step (corresponds to conventional curve type 6).
Transfer Time	Specify the amount of time needed to transfer sample from the first dimension column to the second dimension column. This will be the run time of each first dimension gradient step, unless the step's combined salt divert time and second dimension gradient's run time is greater. Range: 0 to 99.99 minutes.
 Related Topics

More:

Waters 2796 1D Gradient Table Operation


Waters 2796 1D Gradient Table Operation

Adding a Gradient Line to the 1D Gradient Table

Enter a step number, composition, flow rate, salt divert time, 2D table, and any notes specific to the gradient line, click a step and then press the  [image]  toolbar button.

Deleting Single Gradient Line From the 1D Gradient Table

Click a time in the list and then press the  [image]  toolbar button.

Deleting all of the Gradient Lines in the 1D Gradient Table

Press the  [image]  toolbar button. This button is only available when there are lines in the table.

Modifying a Gradient Line

1.	Click a time in the list to select the required line in the 1D Gradient Table. The properties of the line will then be displayed and can be altered as appropriate.

2.	Once changes are complete press the  [image]  toolbar button to re-enter the line into the 1D Gradient Table. If, however, the time value is modified such that it does not correspond to any existing entry in the 1D Gradient Table, pressing  [image]  will result in a new entry.


Waters 2796 2D-X / 1525 Page

Use the 2D-X / 1525 Gradient Table to program up to 10 second dimension gradient lines in Custom Two Dimension Step / Sampling methods, and 15 lines in Single Dimension / Custom Two Dimension methods.

Time	Enter the time at which the specified conditions (composition, flow rate, and curve) should take effect. Range: 0 to 999.99 minutes. Note:  Note: A gradient line with time 0 is always present in the Gradient Table. This line indicates the initial conditions of the gradient.
Solvent E% to Solvent F%	Enter the solvent composition for the specified time. For each gradient line the solvent composition must sum to 100%. Range: 0 to 100%.
Flow	Enter the flow rate for the specified time. Range: 0 to 5 mL/min.
Curve	Specify the rate at which the composition and flow rate should change to the conditions of the gradient line. Curves are specified by number (see illustration). Range: 1 to 11. • 1 - The specified conditions take effect immediately. • 2 to 5 - Convex • 6 - Linear • 7 to 10 - Concave • 11 - The specified conditions take effect at the start of the next gradient line.

The following  fields are only available in Comprehensive Two Dimension Step  methods.

New	Creates a new second dimension gradient, causing a new 2D-X tab to appear.
Delete	Deletes the second dimension gradient, causing the existing 2D-X tabs to be renumbered.
 Related Topics

More:

Waters 2796 2D-X / 1525 Gradient Table Operation


Waters 2796 2D-X / 1525 Gradient Table Operation

Add a Gradient Line to the Gradient Table

 Enter a time, composition, flow rate, and curve type, then press the  [image]  toolbar button.

Deleting a Single Gradient Line from the Gradient Table

Click a time in the list and then press the  [image]  toolbar button.

Deleting all of the Gradient Lines in the Gradient Table

Press the  [image]  toolbar button. This button is only available when there are lines in the table.

Modifying a Gradient Line,

1.	Click a time in the list to select the required line in the Gradient Table. The properties of the line will then be displayed and can be altered as appropriate.

2.	Once changes are complete press the  [image]  toolbar button to re-enter the line into the Gradient Table. If, however, the time value is modified such that it does not correspond to any existing entry in the Gradient Table, pressing  [image]  will result in a new entry.


Waters 2796 Autosampler

Note: 	Note: To control the Waters 2796 autosampler and pump from the keypad rather than the MassLynx software the Inlet must be configured as None.

The Waters 2796 Autosampler pages can be accessed by selecting View, Waters2796 Autosampler from the menu on the Inlet Editor, selecting Autosampler from the shortcut bar, or by pressing the [image] toolbar button.

 Related Topics

More:

Waters 2796 Injection Parameters Page

Waters 2796 Autosampler Parameters Page

Waters 2796 Wash Parameters Page


Waters 2796 Injection Parameters Page

Inject Type	Select the inject type from the drop down list box. • Sequential - Sample aspiration and loop fill occur at the start of each injection cycle, after completion of the previous injection. • Parallel - Sample aspiration and loop fill occur concurrently with other separation method functions for higher throughput. • Manual - For use with a manual injector valve: The autosampler is disabled, and the start of the injection is triggered by a high (load) / low (inject) signal sequence on the Hold Inject 2 analog input.
Fill Mode	Select the fill mode from the drop down list box. • Full Loop - The autosampler draws in the volume of the loop multiplied by the overfill factor, to ensure that the loop is full. • Partial Loop - The autosampler will draw in the volume specified in the sample list and center it in the loop.
Aspirate Air Pre-sample	Enter the volume of air to be drawn into the needle before the sample, to separate it from the previous sample. Range: 0 to 10 µL.
Aspirate Air Post-sample	Enter the volume of air to be drawn into the needle after the sample, to separate it from the next sample. Range: 0 to 10 µL.
Loop Off-line Time	For Parallel Injection mode, specifies the time after an injection when the next sample is preloaded into the sample loop. Preloading the sample into the loop can result in a small decrease in injection-to-injection cycle time. A value of 0 ensures that the next sample will not be preloaded into the sample loop. Values greater than 0 and less than or equal to the method run time will cause the next sample to be preloaded into the sample loop at the given time. However, the time entered should not be less than the time needed for the current sample to leave the sample loop (based on the size of the sample loop and the current flow rate). For Sequential Injection mode there is no "preload" of sample, but the loop can be brought off-line to achieve a decrease in delay volume during the separation. Range: 0 to the Run Time defined on the Pump Mobile Phase page, in minutes.
Overfill Factor	For Full Loop Injection mode enter the number of times to draw the loop volume into the loop to ensure that it is full. Range: 1 to 99.9.
 Related Topics


Waters 2796 Autosampler Parameters Page

Sample Temperature Set	If a sample heater/cooler is installed, enter the temperature to heat or cool the sample to. Range: 4 to 40 °C.
Sample Temperature Limit	Enter the maximum deviation in sample temperature allowed. If this limit is exceeded the current acquisition will stop and the LC Status OK indicator, on the MassLynx screen, will turn red. Range: ±1 to ±20 °C.
Loop Size	This is a display only field showing the volume of the sample loop installed.
Syringe Size	This is a display only field showing the size of the syringe installed.
Draw Depth	Adjusts the draw depth of the needle tip to accommodate for sedimented samples or non-standard wells/vials. A value of 0 corresponds to the bottom of the well. Range: 0 to 20 mm.
Draw Speed	This determines the rate in microliters per second at which sample is drawn into the needle. This should be set according to the viscosity of the sample. Select Fast, Normal, Slow, or Custom from the drop down list box. The table below shows the draw rate for each selection using a 500 µL syringe.
		Selection Fast   Slow Normal  Custom	Draw Rate for a 500 µL Syringe 40 µL/sec  2 µL/sec  5 µL/sec Value entered in the Custom Speed box.
Seek Well Bottom	If this box is checked then, for the first sample drawn from a plate, the needle will automatically seek the bottom of the well before drawing the sample. The depth of the well will be saved by the software and used as the depth for all other wells on the plate. This will be repeated for the first sample drawn from each plate.
Check Plate Height	If this box is checked, for the first injection from a plate, a needle positioning sensor determines the plate height then checks it against the Plate Size, Z value defined in the Plate Generator.


Waters 2796 Wash Parameters Page

Wash Frequency	Select the wash frequency from the drop down list box. • None - Do not perform a wash. • Inject - Perform a wash after each injection. • Well - Perform a wash after all samples have been taken from the current well.
Inject Port	Enter the time in seconds to wash the interior of the needle. Range: 0 to 99.
Needle Exterior	Enter the time in seconds to wash the exterior of the needle. Range: 0 to 99.
Wash Cycles	Enter the number of times the Inject Port and Needle Exterior washes are to be performed. Range: 0 to 10.
Replacement Volume	Enter the volume of purge solvent to deliver through the sample management system after the wash operation has been performed. Range: 0 to 9999 µL.
Wash Sequence	Select Wash - Purge or Purge - Wash - Purge from the drop down list box.
 Related Topics


Waters 2796 Menu

The following features are available through the Inlet Editor menu.

More:

Waters 2796 Wet Prime

Waters 2796 Wash Needle

Waters 2796 Refresh Syringe

Waters 2796 System Preparation

Waters 2796 Bed Layout

Waters 2796 Plate Generator

Creating and Deleting Waters 2796 Plates

Vial Referencing Examples

Waters 2796 Column Configuration

Waters 2796 Peripheral Configuration

Waters 2796 Method Synopsis


Waters 2796 Wet Prime

Wet Prime replaces solvent in the path from the reservoirs through the Prime position of the inject valve to waste.

Note: If the solvent lines are dry, perform the dry prime procedure before continuing. See the Waters 2796 Bioseparations Module Operator's Guide for more information on performing a dry prime.

Flow	The flow rate to use for the wet prime. Range: 0.01 to 10 mL/min.
Time	The amount of time to perform the wet prime. Range: 0 to 999.99 minutes.
Solvent A% to Solvent D%	The composition to use for the wet prime. Range: 0 to 100%.


Waters 2796 Wash Needle

Wash Needle washes the inject port and the needle interior and exterior with wash solvent, and then replaces the wash solvent with purge solvent.

Wash Cycles	The number of wash cycles to perform. Range: 1 to 99.
Inject Port	The amount of time to wash the inject port and the needle interior. Range: 0 to 9999 seconds.
Needle Exterior	The amount of time to wash the needle exterior. Range: 0 to 9999 seconds.
Replacement volume of degassed solvent	The amount of purge solvent to use when replacing the wash solvent. Range: 0 to 9999 µL.


Waters 2796 Refresh Syringe

Refresh Syringe replaces the solvent in the sample management system with fresh purge solvent.

Strokes	The number of syringe strokes to perform. Range: 1 to 99.
Replacement volume of degassed solvent	The amount of purge solvent to use when replacing the sample management solvent. Range: 0 to 9999 µL.


Waters 2796 System Preparation

System Preparation prepares the 2796 Bioseparations Module for operation by filling the entire liquid line pathway with fresh eluents, or wash and purge solvents, according to the solvent composition of the method. The System Preparation function accomplishes this by performing a Wet Prime on each of the solvent lines used by the method, washes the needle and purges the syringe, and leaves the system at the initial conditions of the method.

Standard	Performs a standard System Preparation
Solvent Change	Performs a standard System Preparation as well as an additional Wet Prime on each of the solvent lines used by the method, at 7.0 mL/min.
 Related Topics


Waters 2796 Bed Layout

Use the Bed Layout Editor to define the type, number, and location of the well plates on the 2796 plate carrier. To access the Bed Layout Editor, select Bed Layout from the Waters2796 menu.

Bed Layouts	Lists the available Bed Layouts.
Current Layout	Specifies the bed layout currently in use.
 Related Topics

More:

Deleting a Bed Layout

Creating a New Bed Layout

Modifying a Bed Layout


Deleting a Bed Layout

Highlight the bed layout to delete and press the [image] button. A dialog box will ask you to confirm the deletion. Press the OK button to delete the bed layout.

Note: 	Note: You cannot delete the bed layout which is selected as the Current Layout.


Creating a New Bed Layout

1.	Highlight a bed layout similar to the one you want to create and press the [image] button to create a new layout. The layout appears in the Bed Layouts list as the same name with a 1 at the end, for example Six Position Microtiter1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

3.	If the plate position or type needs changing select the Modify Bed Layout tab.

Note: 	Note: New bed layouts are saved to the MassLynx Racks directory.


Modifying a Bed Layout

Use the Modify Bed Layout page to modify an existing bed layout.

1.	To access the Modify Bed Layout page, click the Modify Bed Layout tab. The Modify Bed Layout page shows a graphical representation of the selected bed layout. There are four plate positions in the 2796.

2.	Click the plate that you want to change to display the Plate Position and Type dialog.

3.	This dialog allows you to select a new plate from a list of possible options, and change its actual position on the bed. Select the plate type you want to use in the bed layout, then click OK.

OpenLynx plate login	If this box is checked and Use current MassLynx autosampler bed layout is checked in the OpenLynx Manager program, then the plate at this position can only be used for plate login on the OpenLynx Login program.


Waters 2796 Plate Generator

To display the Plate Generator dialog, select Plate Generator from the Waters2796 menu.

Plate Name	The name of the plate that is currently being edited.
Rows	The number of vials in a row and the distance between the center of each vial.
Columns	The number of vials in a column and the distance between the center of each vial.
Offsets	Allows alternate vial rows or columns to be offset. Note: Entering a positive value will shift even numbered rows to the right and negative values will shift even numbered rows to the left.
Vial Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Horizontal	Sets the horizontal axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing.
Vertical	Sets the vertical axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing.
Referencing	Select the reference type from the drop down list box. • XY - References the vials A1, B1 etc. • Sequential Discontinuous - Numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous - Numbers the vials 1, 2, 3 across a row, left to right, then continues to number the next row, right to left, etc. If the Waters 2796 autosampler is used with OpenLynx then the vial referencing must be set to either Sequential Continuous or Sequential Discontinuous.
Priority	Check the Horizontal first box if samples are to be acquired horizontally across the plate. • If Referencing = XY, Horizontal = Letter, Vertical = Number and Horizontal Priority is checked, this will result in samples being acquired in the order A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired in the order 1A, 1B, 1C, etc. • If Referencing = Sequential Continuous or Sequential Discontinuous and Horizontal Priority is checked, this will result in samples being acquired from row 1 then row 2. If the Horizontal Priority box is not checked samples will be acquired from column 1, then column 2, etc.
Plate Size	The size of the plate on its outer edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate.
Vial	The depth and diameter values are used for display only. They appear in the description for a single shot login on the OpenLynx Login screen.
 Related Topics


Creating and Deleting Waters 2796 Plates

Creating a New Plate

1.	Press the [image] button. A new default plate is displayed.

2.	Change the Plate Name, enter the appropriate values and press the save [image] button or select Plate, Save Plate. New plates are saved to the MassLynx Plates directory.

Copying a Plate,

1.	Page through the list of saved plates using the [image] and [image] toolbar buttons.  The Previous Plate and Next Plate options on the Plate menu perform the same operation.

2.	When the required plate is displayed change the Plate Name

3.	Enter the appropriate values and press the save [image] button or select Plate, Save Plate. New plates are saved to the MassLynx Plates directory.

Deleting a Plate

1.	 Select the plate, by typing the name in the Plate Name box or by paging through as above

2.	pPress the delete [image] button or choose Plate, Delete Plate .

Note: 	Note: All of the spacings and the Vial section are stored in 0.1 mm units.

Note: 	Note: If the plate currently selected on the Sample Configuration page is changed here, then Reset Injector should be selected from the LC menu to reset communications.

 Related Topics


Waters Systems - Waters 2796 Menu - Vial Referencing Examples
Vial Referencing Examples

The following tables show four examples of vial referencing for a simplified 4 × 3 vial plate.

	1	2	3	4	Horizontal: 123
A	1,A	2,A	3,A	4,A	Vertical: ABC
B	1,B	2,B	3,B	4,B	Referencing: XY
C	1,C	2,C	3,C	4,C	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: 123
A	A,1	A,2	A,3	A,4	Vertical: ABC
B	B,1	B,2	B,3	B,4	Referencing: XY
C	C,1	C,2	C,3	C,4	Priority: Horizontal First NOT Checked
	1	2	3	4	Horizontal: N/A
A	1	2	3	4	Vertical: N/A
B	5	6	7	8	Referencing: Sequential Discontinuous
C	9	10	11	12	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: N/A
A	1	6	7	12	Vertical: N/A
B	2	5	8	11	Referencing: Sequential Continuous
C	3	4	9	10	Priority: Horizontal First NOT Checked
 Related Topics


Waters 2796 Column Configuration

To display the Column Configuration dialog, select Column Configuration from the Waters2796 menu.

Column Switch	This is a display only field that describes the column configuration of the 2796. For example: 6 Position.
Column 1 to Column 6	Enter a description of columns 1 through 6 (if installed).
 Related Topics


Waters 2796 Peripheral Configuration

To display the Peripheral Configuration dialog, select Configuration from the Waters2796 menu.

1525 HPLC Pump Present	Check this box to indicate that a 1525 is present in the system. Note: This box is automatically checked in Comprehensive Two Dimension Step / Sampling mode, and cannot be changed.
Use As Primary Flow	Check this box to display the status of the 1525 on the main MassLynx LC Status bar, and to use the 1525 flow rate as the flow rate for FractionLynx fraction collection.
1525 HPLC Pump Head Size	Select the 1525 head size from the drop list box: 50 µL, 100 µL, or 225 µL (currently limited to 50 µL).
Auxiliary Valve 1 to Auxiliary Valve 3	Check these boxes to indicate that the given auxiliary valve is present in the system. Note: Auxiliary Valve 1 is automatically checked in Comprehensive Two Dimension Step / Sampling mode, and cannot be changed.
 Related Topics


Waters 2796 Method Synopsis

(Comprehensive Two Dimension Step / Sampling Methods Only)

To display a synopsis of the Comprehensive Two Dimension Step / Sampling method, select Method Synopsis from the Waters2796 menu. The synopsis contains the details of any MassLynx generated events in the 2796 gradient table,  1525 gradient table, and  2796 timed event table.

 Related Topics


Waters CapLC System Status Pages

The System Status pages display information about the state of the machine being controlled. These pages can be accessed within the Inlet Editor by selecting View, Status, selecting Status from the short cut bar or by pressing the [image] toolbar button.

More:

Waters CapLC Solvent Status Page

Waters CapLC Valve Status Page

Waters CapLC PDA Status Page


Waters CapLC Solvent Status Page

Indicators	The Running, Pump On and Injector Cycle indicators at the left of the screen give information on the current status of the LC system. The OK and Ready Indicators become illuminated in red if the LC System has an error. Click on the red indicators to display more information on the cause of the malfunction.
Time	This displays how long the method has been running
Flow	This displays the current flow rate as returned by the instrument.
Pressure	This displays the current pressure in the instrument. To the right of the Time, Flow and Pressure fields is a display of the solvent percentages at which the LC System is currently operating.
Column	This displays the current temperature of the column.
Sample Temp	This displays the current temperature of the sample.
 Related Topics


Waters CapLC Valve Status Page

This page shows what position the Valves are currently set to, if installed.

See the Waters Cap LC Users' Guide for details of the valves.

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Waters CapLC PDA Status Page

Current State	This displays the current state of the PDA Detector
Scan Number	When acquiring diode array data this displays the number of scans currently acquired.
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Waters CapLC Pump

The Waters Pump pages can be accessed by selecting View, Waters CapLC Pump or by pressing the [image] toolbar button.

Before using the CapLC pump itn needs to be plumbed in see Waters CapLC Plumbing DiagramsWatersCapLCPlumbingDiagramsPlumbing.

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Waters CapLC Initial Conditions Page

Waters CapLC Gradient Page

Waters CapLC Initial Events Page

Waters CapLC Timed Events Page

Waters CapLC Chart Recording Page

Waters CapLC Method Type Page


Waters CapLC Initial Conditions Page

Solvent Select A1 to A3	Select the solvent to deliver through Pump A.
Solvent B and C	Enter the percentage of solvent flow from pump B and/or C (if installed).
Solvent Name	Enter the name of the solvent in the corresponding solvent reservoir.
Flow	Enter the total flow rate for the system in μl/min.
Run Time	Enter the length of time (in minutes) until the next injection occurs. Note: Run time is for the pump and autosampler only. Detectors have independent run times. The MS method run time must be greater than all other run time (see The Function List Editor chapter for details). Note: If you are running a gradient or setting timed events, make sure you set the initial conditions Run Time to a value greater than or equal to the greatest Time value in the Gradient or Timed Events Table.
Low Pressure	Enter the low-pressure limit for the system. If the system pressure falls below this limit, the flow stops and the LC Status error light turns red. Range: 0 to 4500 psi.
High Pressure	Enter the high-pressure limit for the system. If the system pressure exceeds this limit, the flow stops and the LC Status error light turns red. Range: 0 to 5000 psi.
Temperature	Enter the target operating temperature for the optional column heater. This value must be at least 5 C above ambient. Range: 20 to 60 C. Minimum setting: 5 C above ambient.
Range	Enter the maximum allowable temperature deviation from the value set for the column heater temperature. If the column heater temperature deviates beyond the specified range, the run stops and the LC Status error light turns red. Range: ±0.0 to ±10.0 C.
Name .	Enter the name of the installed column
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Waters CapLC Gradient Page

Use the Gradient Table to define conditions for a gradient run. For each row in the Gradient Table, define the percent composition of up to four solvents that are to be delivered at the desired flow rate for the specified time. Enter the number of the gradient curve required. This defines how changes to solvent percentages and flow rates take place over the elapsed time of each gradient segment (the time that elapses between the start time of one row and the start time of the next row).

Note: For an isocratic run, set the solvent percentages, run time and flow on the Initial Conditions page. Do not add any rows to the Gradient Table.

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Waters CapLC Gradient Table Parameters

Waters CapLC Gradient Table Operation


Waters CapLC Gradient Table Parameters

Time (mins)	Specifies when the conditions (%A-%D, Flow, and Curve) for the row take effect. Make sure the Time for the first row is set to 0.00 to establish initial conditions for the gradient run. Range for rows other than row 1: 0.01 to 999.99 minutes
B% and C%	Specifies the percentage of solvent flow from each reservoir. For each row, the total of all solvents must equal 100%. Range: 0 to 100% Note: Percent flow for reservoir A is not displayed. Percent A is calculated as: 100% - (B% + C%)
Flow (μl/min)	Specifies the total flow rate for the system.
Curve	Specifies the rate of change of solvent composition and flow rate over time, based on the curve number and the length of the gradient segment. For more information, see Gradient Curves, below and  Waters 2690/2695 Pump Gradient Page.
Curve Number	Effect
1	Immediately goes to specified conditions
2 to 5	Convex
6	Linear
7 to 10	Concave
11	Maintains start condition until next step
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Waters CapLC Gradient Table Operation

To add a gradient, enter a time, percentage, flow rate and curve number in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being created.

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Waters CapLC Initial Events Page

Use the Initial Events page to set the initial condition of the two contact-closure output switches, the initial position of the stream select valve, and the initial position of the optional diverter valve.

Note: To change the settings of these switches and valves during a run, use the Timed Events Table.

Switch 1 and 2	Select the initial state of contact-closure Switch 1 and 2 from the drop down list boxes.
Stream Select	Select the initial state of the stream select valve (Position 1 or 2) from the drop down list box.
Diverter	Select the initial position of the optional diverter valve (System or Vent) from the drop down list box.
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Waters CapLC Timed Events Page

Use the Event Table to program up to 16 events (both external and internal). The external events are triggered by four contact closures (relays) through output terminals (S1-S4) on the 2790/2795 Separations Module. The internal events are used to control the sample compartment temperature, column heater temperature, and to prime and flush the 2790/2795 Separations Module. Events can be triggered more than once and multiple events can be triggered simultaneously.

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Waters CapLC Event Table Parameters

Waters CapLC Switch States

Waters CapLC Event Table Operation


Waters CapLC Event Table Parameters

Time	Enter the time (after injection) at which the event starts. Event rows are sorted automatically by time. Note: Different events can be programmed to occur at the same time. Range: 0.00 to 999.99 min.
Event	Select the type of event signal: one of the two contact-closure output switches (Switch1or Switch 2), or one of the internal events (Set temperature, Stream Select or Vent Valve). Choose from these event types to program up to 16 events. Note: The same event can be programmed more than once. Available choices: • Switch 1 and 2 Corresponds to terminal strip positions S1 and S2 on the rear of the unit. Activating a Switch event triggers a contact closure for controlling an external device. Select a switch event and a state for the switch (On, Off, Toggle, Pulse or No Change). This state appears in the Action column of the table (see Switch States, below). Note: If Pulse is selected for a "switch state" the duration of the pulse must be entered in the Width (min) field. • Set Temperature Specifies the temperature of an optional column heater. If Set Temperature is selected for a switch state the temperature in (C) must be entered in the Column Temperature field. Note: When this event occurs, the temperature of the column heater changes from the value set on the Initial Conditions page to the value set for the event. When the event times out, the temperature returns to the value on the Initial Conditions page value. • Stream Select (1 or 2) Specifies the position of the stream select valve. • Vent Valve (System or Vent) Specifies the position of the vent valve.
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Waters CapLC Switch States

•	On - Turns on a contact closure that triggers an external or internal event. With this function, the contact closure remains closed until an Off function is sent.

•	Off - Turns off the contact closure for the event. With this function, the contact closure is broken.

•	Toggle - Changes the current state of the switch.

•	Pulse - Transmits a single On/Off pulse. The contact closure is maintained for the time entered in the Width box. Range: 0.01 to 100.00 minutes.

•	No Change - Leaves the switch in its current state.

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Waters CapLC Event Table Operation

To add an event, enter a time, event, action and value in the relevant boxes and press the [image] toolbar button. Note the first entry must have a time of 0.

To delete a single event click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being created.

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Waters CapLC Chart Recording Page

Use the Chart Recording page to select up to two analog signals to be output to an external device such as an integrator or strip-chart recorder. Select one of the following the signals to output, from the drop down list box.

•	None

•	Flow

•	Pressure

•	Percent A, B, or C

•	Column temperature

Note: To record a signal, you need to connect each external device to the appropriate Chart Out terminal pair on the rear of the unit. Refer to the Waters CapLC System Installation and Maintenance Guide for installation and specification details.

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Waters CapLC Method Type Page

Specifies the type of method to create. Select one of:-

Normal Method	The Method Type used for standard injections. Ensure that the Method Type is set to Normal unless you are performing one of the procedures listed below.
Column Condition Method	Runs solvent through the column without injecting samples or running the Events table. Solvent is delivered using the gradient table specified in the Gradient page.
Equilibrate Method	Delivers solvents and maintains solvent parameters using the values defined on the Initial Conditions page.
Wet Prime	Replaces solvent in the tubing with fresh solvent from the reservoirs through the Prime port of the inject valve to waste. Use a Wet Prime Method when changing the solvents in the system. Check the boxes for the solvent lines to prime, and the number of loop volumes to use. Waters recommends starting the wet prime using the solvent with the lowest viscosity to help purge air from the lines, especially if the in-line vacuum degasser is installed. Note: If the solvent lines in the CapLC are dry, you must perform the dry prime procedure before performing a wet prime.
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Waters CapLC Autosampler

These pages are used to set parameters specific to the Autosampler, to access them select View, WatersCapLC AutoSampler, select Autosampler from the short cut bar or press the [image] toolbar button.

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Waters CapLC AutoSampler Page

Waters CapLC Mix Method Page

Waters CapLC Bed Layout

Waters CapLC Plate Generator

Creating and Deleting Waters CapLC Plates

Waters CapLC Plate Feeder


Waters CapLC AutoSampler Page

Draw Height	Adjusts the depth of the needle tip to accommodate for sedimented samples. A value of 0 corresponds to the top of the plate carrier. Range: 0 to 40 mm.
Draw Speed	Select the draw rate of the syringe from the drop down list box. The different rates accommodate for samples of varying viscosity. The rate for each selection is dependent on the size of the installed syringe. The table below shows the draw rates for each selection.
	Draw Rate for  25 l Syringe	Draw Rate for  100 l Syringe	Draw Rate for  250 l Syringe	Draw Rate for 500 l Syringe
Fast	94 l/min	375 l/min	940 l/min	1875 l/min
Normal	63 l/min	250 l/min	625 l/min	1250 l/min
Slow	32 l/min	375 l/min	315 l/min	625 l/min
Injection Type	Select one of the following injection types from the drop down list box: Full Loop - The sample loop is completely filled. Partial Loop - The sample loop is partially filled with the volume defined in the Sample List. The value in the Sample List must not exceed the Full Loop volume. µl Pickup - The sample loop is filled with only the amount of sample to be injected (resulting in no sample loss). Sample is transported into the loop by transport liquid (mobile phase) from the transport vial. Manual - Specifies that the manual injector is used (the autosampler is disabled). Switching the manual injector to the Inject position initiates any programmed gradients and/or timed events.
Flush Volume	Enter the volume (in microliters) of sample taken from a vial before the loop is filled with sample. This flushes out previous samples.
Head Space Pressure	If this box is checked the prepuncturing needle will put approximately 0.5 bar of pressure on the sample to stop formation of air or vapour bubbles. Enable this parameter only when using sample vials with air-tight caps.
Air Space Segment	If this box is checked an air segment is added to the front of the flush volume to minimize dilution and bandspreading and reduce the amount of flush volume required. In Full and Partial Loop modes, the air segment is flushed to waste; in µl Pickup mode, the air segment is injected. Disable this parameter if the air segment causes problems in µl Pickup mode.
High Efficiency Mode	If this box is checked the sample loop will be taken out of the flow stream after the sample has been flushed, but before the gradient front reaches the injection valve.
Wash Volume	Enter the volume (in microliters) of wash solvent used to clean the needle and buffer tubing.
Sample Temperature	Enter the target operating temperature for the optional sample heater/cooler Range: 4.0 to 40.0 C.
Temperature Limit	Enter the maximum allowable temperature deviation from the value set for the Sample Temperature. If the sample temperature deviates beyond the specified range, the LC Status error light turns red and the run stops.  Range: ±1.0 to ±20.0 C.
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Waters CapLC Mix Method Page

Mix Delay	Enter the delay time before mixing, in minutes. A value of 0 corresponds to the top of the plate carrier. Range: 0 to 99.9 mins.
Mix Cycles	Enter the number of times to perform the Mix operation.
Reagent Position 1	Enter the position of the first reagent to mix.
Volume Reagent 1	Enter the volume of reagent 1 to mix.
Reagent Position 2	Enter the position of the second reagent to mix.
Volume Reagent 2	Enter the volume of reagent 2 to mix.


Waters CapLC Bed Layout

Use the Bed Layout Editor to define the type, number, and location of the well plates on the CapLC plate loader. To access the Bed Layout Editor, select Cap LC Tools, Bed Layout.

Bed Layouts	Lists the available Bed Layouts.
Current Layout	Specifies the bed layout currently in use.
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To Delete A Bed Layout (Waters CapLC)

To Create A New Bed Layout (Waters CapLC)

To Modify a Bed Layout (Waters CapLC)

Other Bed Layout Options (Waters CapLC)


To Delete A Bed Layout (Waters CapLC)

Highlight the bed layout to delete and press the [image] button. A dialog box will ask you to confirm the deletion. Press the OK button to delete the bed layout.

Note: You cannot delete the bed layout that is selected as the Current Layout.

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To Create A New Bed Layout (Waters CapLC)

1.	Highlight a bed layout similar to the one you want to create and press the [image] button. The layout appears in the Bed Layouts list as the same name with a 1 at the end, for example Six Position Microtiter1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

3.	If the plate position or type needs changing select the Modify Bed Layout tab.

Note: New bed layouts are saved to the MassLynx Racks directory.

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To Modify a Bed Layout (Waters CapLC)

Use the Modify Bed Layout page to modify an existing bed layout. To access the Modify Bed Layout page, click the Modify Bed Layout tab. The Modify Bed Layout page shows a graphical representation of the selected bed layout.

Click on the plate that you want to change to display the Plate Position and Type dialog.

This dialog allows you to select a new plate from a list of possible options, and change its actual position on the bed. Select the plate type to use in the bed layout, then click OK.

OpenLynx plate login	If this box is checked and Use current MassLynx autosampler bed layout is checked in the OpenLynx Manager program, then the plate at this position can only be used for plate login on the OpenLynx Login program.
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Other Bed Layout Options (Waters CapLC)

1.	To append a new column, press the [image] button.

2.	To delete the current column press the [image] button.

3.	To insert a column, click on the column before which you want to insert and press the [image] button. Note: The column inserted will have the same number of rows as the column highlighted.

4.	Note: The number of rows in a column cannot be changed and so the [image] button is grayed out.

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Waters CapLC Plate Generator

To display the Plate Generator dialog, select CapLC Tools, Plate Generator.

Plate Name	The name of the plate that is currently being edited.
Rows	The number of vials in a row and the distance between each center
Columns	The number of vials in a column and the distance between each center.
Offsets	Allows alternate vial rows or columns to be offset. Note: Entering a positive value will shift even numbered rows to the right and negative values will shift even numbered rows to the left.
Vial Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Horizontal	Sets the horizontal axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing. Default: numeric.
Vertical	Sets the vertical axis of the plate as either alphabetic (ABC) or numeric (123), when using XY referencing. Default: alphabetic.
Referencing	This has three options  • XY which references the vials A1, B1 etc. • Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to right, then continues number the next row, right to left etc. If the Waters CapLC autosampler is used with OpenLynx then the vial referencing must be set to either sequential continuous or sequential discontinuous.
Priority	Check the Horizontal First box if samples are to be acquired horizontally across the plate. If Referencing = X,Y and Horizontal First is checked, then the horizontal value be read first when referencing a vial (1,A). If Horizontal First is not selected, then the vertical value be read first when referencing a vial (A,1). Default: Horizontal First selected. If Referencing = Sequential Continuous or Discontinuous and Horizontal First is checked, then vials will be numbered horizontally. This will result in samples being acquired from row 1 then row 2. If Horizontal First is not checked, then vials will be numbered vertically. This will result in samples being acquired from column 1 then column 2 etc. Default: Horizontal First selected.
Plate Size	The size of the plate to its outside edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate.
Vial	The depth and diameter values are used for display only. They appear in the description for a single shot login on the OpenLynx Login screen.
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Creating and Deleting Waters CapLC Plates

To create a new plate, press the [image] button. A new default plate is displayed, change the Plate Name, enter the appropriate values and press the save [image] button or select Save Plate from the Plate menu. New plates are saved to the MassLynx Plates directory.

To copy a plate, page through the list of saved plates using the [image] and [image] toolbar buttons. The Previous Plate and Next Plate options on the Plate menu perform the same operation. When the required plate is displayed change the Plate Name, enter the appropriate values and press the save [image] button or select Save Plate from the Plate menu. New plates are saved to the MassLynx Plates directory.

To delete a plate select the plate, by typing the name in the Plate Name box or by paging through as above, and press the delete [image] button or choose Delete Plate from the Plate menu.

Note: All of the spacings and the vial section are stored in 0.1 mm units.

Note: When defining a custom plate for use with a multi-injector the plate is required to be compatible with the position of the 8 needles of the autosampler.

•	The Plate must have eight columns.

•	The position of the vials should allow all eight needles to enter a separate vial.

•	There should be no odd or even offsets for any of the vial positions.

Note: If the Plate currently selected on the Sample Configuration page is changed here, then Reset Injector should be selected from the LC menu to reset communications.

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Vial Referencing Examples


Waters Systems - Creating and Deleting Waters CapLC Plates - Vial Referencing Examples
Vial Referencing Examples

The following tables show four examples of vial referencing for a simplified 4 × 3 vial plate.

	1	2	3	4	Horizontal: 123
A	1,A	2,A	3,A	4,A	Vertical: ABC
B	1,B	2,B	3,B	4,B	Referencing: XY
C	1,C	2,C	3,C	4,C	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: 123
A	A,1	A,2	A,3	A,4	Vertical: ABC
B	B,1	B,2	B,3	B,4	Referencing: XY
C	C,1	C,2	C,3	C,4	Priority: Horizontal First NOT Checked
	1	2	3	4	Horizontal: N/A
A	1	2	3	4	Vertical: N/A
B	5	6	7	8	Referencing: Sequential Discontinuous
C	9	10	11	12	Priority: Horizontal First Checked
	1	2	3	4	Horizontal: N/A
A	1	6	7	12	Vertical: N/A
B	2	5	8	11	Referencing: Sequential Continuous
C	3	4	9	10	Priority: Horizontal First NOT Checked
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Waters CapLC Plate Feeder

To display the Plate Loader dialog, select Plate Loader from the CapLC Tools menu.

The Plate Loader dialog is used when a plate needs to be changed.

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Waters CapLC PDA Detector

This page is used to set parameters specific to the UV detector, to access it select View, WatersCapLC PDA Detector, select Detector from the short cut bar or press the [image] toolbar button.

Start Wavelength	Enter the wavelength at which to start acquiring data. Range (with Resolution set to 1.2): 190.0 nm to 800.0 nm. Range (at all other Resolution settings): 190.0 + (Resolution/2) to 800.0 - (Resolution/2). Default: 200 nm.
End Wavelength	Enter the wavelength at which to stop acquiring data. Range with Resolution set to 1.2: Start Wavelength to 800.0 nm. Range at all other Resolution settings: Start Wavelength + Resolution to 800.0 nm - Resolution/2.
Resolution	Enter the number of diodes to be averaged together as a single spectral data point. To differentiate closely related spectra and obtain greater spectral resolution, use a small resolution number. Be aware, however, that a small resolution value generates more data points and therefore requires more disk space than a large resolution value. Find a resolution value just small enough to identify spectral features. Range: 1.2 to 24.0 nm in multiples of 1.2.
Sampling Rate	Select the acquisition rate in spectra per second from the drop down list box. For good integration and quantitation, acquire 15 to 20 spectra across a peak.
Auto Exposure	Check this box to enable the detector optics to calculate the optimum exposure time needed to recharge the diodes based on the lamp energy, the lamp spectrum and the selected wavelength range. Tip: Enable Auto Exposure for most routine analyses.
Interpolate	Check this box to instruct the detector to ignore the signal from the photodiode at 656 nm and to interpolate a value from the adjacent diodes. This prevents over-saturation at 656 nm (Balmer line for deuterium). If this box is not checked the detector reports the signal from the photodiode at 656 nm. Disable this parameter only if you are working with compounds that absorb in the 656 nm range. Note: If this parameter is unchecked, the deuterium lamp high emission line at 656 nm may cause spectral artifacts and autoexposure errors.
Exposure Time	Enter the length of time in milliseconds that the photodiodes are exposed to light before they are read. This parameter is not accessible if Auto Exposure is checked. Range: 11.00 to 500.00 ms.
Stop Time	Enter the time, in minutes after injection, when the PDA will stop scanning. This value is independent of the instrument method run time.
Filter Response	Enter the response time (in seconds) for filtering acquired data. The filter is an enhanced rolling average filter applied to absorbance data from the PDA detector before the data is sent to the MassLynx software. The filter reduces high-frequency noise across the entire wavelength range specified for the acquisition. High values decrease peak response. Range: 0 to 3.
Save to Disk	Check this box to save the Photo Diode Array data to the raw datafile. If this data is not required for further processing then uncheck the box, the data is not saved to disk thus reducing the size of the file.
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Waters CapLC Channel Detector Configuration Pages


Waters CapLC Channel Detector Configuration Pages

The Channel 1 and Channel 2 pages contain the same information. Select the page relevant to the channel required, by clicking on the tab.

Output Mode	Select one of: Off - no analog output signal. Absorbance - Output represents absorbance at the wavelength specified by the Wavelength parameter (see below). Note: Ratio Denominator Wavelength and Threshold parameters are not accessible when Absorbance mode is selected. Ratio - Output represents the ratio of absorbances at two wavelengths. The numerator wavelength is specified by the Wavelength parameter, and the denominator wavelength is specified by the Ratio Denominator Wavelength parameter (see below).
Wavelength	Enter the output wavelength. In Ratio mode, the absorbance at the Wavelength is used to calculate ratio in the formula: Ratio = Absorbance at Wavelength/Absorbance at Ratio Denominator Wavelength  Wavelength must be within the wavelength range specified by the Start Wavelength and End Wavelength parameters on the PDA page. Range when Resolution is set to 1.2: Start Wavelength to End Wavelength. Range at all other Resolution settings: Start Wavelength + (Bandwidth/2) to End Wavelength - (Bandwidth/2).
Ratio Denominator Wavelength	Enter the denominator wavelength (in nanometers) for the analog output channel. Ratio Denominator Wavelength must be within the wavelength range specified by the Start Wavelength and End Wavelength parameters in the 996 PDA page.
Bandwidth	Enter the spectral bandwidth of the analog output channel. Range: 1.2 to 24.0 nm in multiples of 1.2.
Filter Type	Select the filter type (Hamming or Single Pole) from the drop down list box for use on the analog output channel. The Hamming filter is designed to create the same degree of peak-height degradation as the Single Pole filter for the same response time, but enhances filtering of high-frequency noise.
Filter Response	Enter the response time in seconds for the Filter Type specified above. Range: 0 to 5 seconds.
Offset	If required enter an offset to the analog output channel. Range: -0.2 to 2.0 AU.
Threshold	Enter a threshold above which the ratio (Wavelength / Ratio Denominator Wavelength) must be to be valid data. The range is -0.1 to 2.0 AU. Note: If no ratio is plotted (one or both channels are below the current Threshold), enter a lower Threshold value.
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Waters CapLC Plumbing Diagrams

The following diagrams are examples of possible plumbing configurations on the CapLC

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Example 1

Example 2

Example 3

Example 4


Example 1

Plumbing arrangement for use with a precolumn only. Allows fast chromatography experiments to be performed.

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Example 2

Plumbing arrangement for precolumn plus analytical column where splitting is not required. For columns of inside diameter 180 micron to 1mm.

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Example 3

Plumbing arrangement for precolumn plus analytical column where splitting is required. For columns of inside diameter less than 180 micron.

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Example 4

Plumbing arrangement for 2D LC experiments with splitting.

Note:  The difference between this set up and example 3 is the insertion of SCX cartridge between the autosampler and the switching valve. The no split version could easily be adapted in the same way to perform 2D should higher flow reversed phase steps be desired.

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Waters 515 and 1525 Pumps

The Waters 515 and 1525 Pump pages can be accessed by selecting View, Waters 515 Pump or Waters 1525 Pump, selecting Inlet from the short cut bar or by pressing the [image] toolbar button.

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Waters 515/1525 Initial Conditions Page

Waters 515/1525 Initial Events Pages

Waters 515/1525 Timed Events Page

Waters 515/1525 Method Type Page


Waters 515/1525 Initial Conditions Page

Solvent A	Enter the name of the solvent that will be delivered through Pump A.
Solvent B	Enter the name of the solvent that will be delivered through Pump B and enter the percentage of the solvent flow from Pump B.
Flow (ml/min)	Enter the total flow rate for the solvent delivery system.  Range: 1 to 10 ml/min.
Run Time	Enter the time in minutes that the method will run, from the point of injection. Note: If running a gradient or setting timed events, make sure the Run Time value is greater than, or equal to the greatest Time value, specified on the Gradient or Timed Events pages.
Low Pressure	Enter the low pressure limit for the system. If the pressure falls below this limit, the solvent flow will stop and the LC status light will turn red.
High Pressure	Enter the high pressure limit for the system. If the pressure exceeds this limit, the solvent flow will stop and the LC status light will turn red.
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Waters 515

Waters 515/1525 Gradient Page


Waters Systems - Waters 515/1525 Initial Conditions Page - Waters 515
Waters 515

If a Waters 515 Pump was selected, the Auxiliary Pump Solvent options are displayed:

Flow (ml/min)	Enter the total flow rate for the auxiliary solvent delivery system.  Range: 1 to 10 ml/min.
Name	Enter the name of the solvent that will be delivered through the auxiliary pump.
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Waters 515/1525 Gradient Page

Use the Gradient Table to define conditions for a gradient run. For each row in the Gradient Table, you need to define the % composition of up to two solvents that are to be delivered at the desired flow rate for the specified Time.

Note: For an isocratic run, set the solvent percentages, run time and flow, on the Initial Conditions page. Do not add any rows to the Gradient Table.

To add a gradient, enter a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient, click with left mouse button on a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes to the left of the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

Flow	Enter the flow rate for the solvent delivery system.
Curve	Enter the number of the gradient curve required. This sets the rate at which the solvent is to change to the new proportions and/or flow rates. See the Waters Operator's Guide for a list of values.
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Waters 515/1525 Initial Events Pages

The external events are triggered by four contact closures (relays) through output terminals, which are located at the back of the instrument.

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Waters 515

Waters 1525


Waters Systems - Waters 515/1525 Initial Events Pages - Waters 515
Waters 515

Relays 1 and 2	From the drop down list box, select ON or Off to activate or deactivate the relay.
Events 1 to 4	From the drop down list box, select ON or Off to activate or deactivate the event.
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Waters 1525

Relays 1 to 4	From the drop down list box, select ON or Off to activate or deactivate the relay.
 Related Topics


Waters 515/1525 Timed Events Page

Use the Event Table to program up to 16 events (both external and internal). Events can be triggered more than once and multiple events can be triggered simultaneously.

Time	Enter the time (after injection) at which the event starts. Event rows are sorted automatically by time.  Note: Different events can be programmed to occur at the same time. Range: 0.00 to 999.99 min.
Event	Select an Event or Relay from the drop down list box.
Switch States	On Turns on a contact closure that triggers an external or internal event. With this function, the contact closure remains closed until an Off function is sent. Off Turns off the contact closure for the event. With this function, the contact closure is broken.
 Related Topics

More:

Event Table Operation


Event Table Operation

To add an event, enter a time, event, action and value in the relevant boxes and press the [image] toolbar button. Note the first entry must have a time of 0.

To delete a single event, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created.

 Related Topics


Waters 515/1525 Method Type Page

Method Type	Specifies the type of method to create.
Normal Column Method	The Method Type used for standard injections. Ensure that the Method Type is set to Normal unless you are performing one of the procedures listed below.
Condition Method	Runs solvent through the column without injecting samples or running the Events table. Solvent is delivered using the gradient table specified in the Gradient page.
Equilibrate Method	Delivers solvents and maintains solvent parameters using the values defined on the Initial Conditions page
Run Event Table	Check this box to run the table of timed events during the method. This option is only active if the Normal or Column Condition Methods are selected.
 Related Topics


Hewlett Packard 5890 Gas Chromatograph

Both the HP5890 Series I and Series II can be controlled by MassLynx. For the Series II instrument it is necessary to configure the GC to respond to Series I commands by setting a jumper in the GC. A Micromass installation engineer will have already done this. Before starting to use the GC the software must be configured to reflect the GC equipment in use e.g. the number of injectors and detectors etc.

Note: The HP 5890 has to be selected on installation.

More:

To change GC Parameters Chromatograph

To Change GC Configuration (Hewlett Packard 5890 Gas Chromatograph)Chromatograph


To change GC Parameters Chromatograph

1.	Choose Configue, Select Interface, GC (TP RS232) from the Acquisition Control Panel.

or

Double click on the picture of the GC on the Acquisition Control Panel to bring up the HP5890 inlet editor shown below.

2.	Make any changes to the parameters. Note: The oven temperature ramp can be modified either by using the keyboard to type in times, temperatures and rates, or by dragging the small red handles on the graph itself using the mouse.

3.	Save the method using either Save or Save As from the File menu.

The time and temperature range of the oven temperature ramp can be controlled using the buttons that appear to the right of the ramp. Clicking on [image] will increase the range shown on the time axis, clicking on [image] will increase the range shown on the temperature axis. Clicking on [image] alters the display ranges so that the oven temperature display fills the graph.

A full description of all the parameters in this editor is given in the HP5890 Gas Chromatograph Reference Manual.


To Change GC Configuration (Hewlett Packard 5890 Gas Chromatograph)Chromatograph

1.	Choose Configuration from the HP5890 Edit menu to display the configuration editor shown below.

2.	Make any changes to the parameters.

3.	Press OK. The parameters will be saved with the GC method when either Save or Save As is selected from the HP5890 File menu. Buttons in the HP5890 Edit menu that are not appropriate for the selected configuration will be grayed out.

The main HP5890 editor is used to set up the GC oven temperature program and to control the dump valve and cryogenic cooling options if fitted.


Hewlett Packard 7673A Auto Injector

The HP 7673A auto injector can only be used with the HP 5890 gas chromatograph.

Note: This dialog only applies if the Dice option is selected at setup, if the Dice option is not selected a "No parameters to set" message is displayed.

More:

To Change Autosampler parameters (Hewlett Packard 7673A Auto Injector)


To Change Autosampler parameters (Hewlett Packard 7673A Auto Injector)

1.	Choose Set up Auto Injector from the Acquisition Control Panel Instrument menu

or

Double click on the picture of the auto injector on the Acquisition Control Panel to display the HP7673A editor shown above.

2.	Make any changes to the parameters.

3.	Save the method using either Save or Save As from the File menu.

A full description of all the parameters in this editor is given in the HP7673A Automatic Sampler Operating Manual.

An autosampler will usually be used with the multiple sample acquisition page where further information such as bottle number will be entered. Starting an acquisition with an autosampler will be covered in the next section


Hewlett Packard HPLC Systems

The HP1050, HP1090 and HP1100 HPLC systems can be controlled from MassLynx. All three photo diode array (PDA) and UV detectors are supported.

The software can be used, to control the pump during instrument tuning, or acquisition and can be used to provide multi-sample acquisitions. Both isocratic and gradient modes of operation are supported.

The HP1050 is described in the examples below. Differences for the HP1090 and HP1100 are also described. On installing the HP1100 the program will automatically detect whether the G1367A Well Pate Autosampler or one of the older HP 1100 autosamplers (G1313 or G1329 is installed and will configure the Inlet Editor accordingly. For a full description of the HP1100 G1367A.

More:

Hewlett Packard Sampler Configuration Page

Hewlett Packard Sampler External Events Page

Hewlett Packard Pump Initial Conditions Page

Hewlett Packard Pump Gradient Timetable Page

Hewlett Packard Pump External Events Page


Hewlett Packard Sampler Configuration Page

Select View, HP1050 AutoSampler, HP1090 AutoSampler or HP1100, Autosampler from the short cut bar or press the [image] toolbar button.

Injection Volume	This is the volume in microlitres to inject. Note: If you are running from the Sample List the injection volume in the sample list entry overrides the setting defined here.
Draw Speed	This determines the rate in microlitres per minute at which sample is extracted into the autosampler needle. This should be set according to the viscosity of your sample.
Eject Speed	This is the speed in microlitres per minute at which sample is ejected from the needle on injection. Again set this according to the viscosity of the sample. Consult your HP documentation for further information.  Note: This facility is only available with the HP1050 and HP1100 and will not be visible on an HP1090 system.
Draw Position	This is an offset value in mm from position 0 and determines how far the needle is inserted into your sample. Consult your HP documentation for further information. Again this facility is only available with the HP1050 and HP1100 and will not be visible on an HP1090 system.
Stop Time	This value is set in minutes to be the time that the autosampler method will run after injection. This does not apply to the HP1090 since this has an in-built autosampler.
External Vial Tray	If an external vial tray is used check this box.
Vial number	The vial to inject from. Note: If a multisample acquisition is being run from the MassLynx Sample List, the Bottle # entry in the sample list overrides the value defined in the Vial Number box.
Syringe Size	Set this to the size of syringe fitted on the HP1090 LC System. This parameter applies to the HP1090 only and will not be visible in a HP1050 or HP1100 system.
Thermostat On	If the autosampler is fitted with a sample heater then this box will be enabled. Check it to use the sample heater. This parameter applies to the HP1100 only and will not be visible in a HP1050 or HP1090 system.
Sample Temperature	Enter the temperature to heat the sample to. This parameter applies to the HP1100 only and will not be visible in a HP1050 or HP1090 system.


Hewlett Packard Sampler External Events Page

External events allow control of the external contacts found on the HP1050 and HP1090 LC systems. In addition HP1090 column switching can also be controlled. For the HP1100 a separate contact board must be installed in the pump in order to use this functionality.

The contacts can be set to operate under timed control during a method run, as well as having their initial states set. The contacts will be in the initial state before a method run and will return to this state after a method has completed.

To add an event, enter a Time, select an Event Type from the drop down list box and press the [image] toolbar button.

To delete a single event click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To change the State of a contact, double click on the time entry in the list to toggle between states.

Time	The time in minutes at which the contact event should occur.
Event	The contact event to be performed.
State	The state determines whether the contact is to be opened or closed.


Hewlett Packard Pump Initial Conditions Page

Select the View,HP1050 Pump, HP1090 Pump or HP1100 Pump, Inlet from the short cut bar or press the [image] toolbar button.

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B, C, D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Flow	This is the total flow rate of the solvent channels according to how you have configured the instrument.
Pressures	These set the upper and lower limits of the pressure within the solvent delivery system (SDS) if the pressure falls outside of this range the SDS switches off.
Column Heater	If the instrument has an oven present then the column temperature can be set to a specified temperature in degrees centigrade. Check the Column Temperature box and enter a temperature. If the software has been configured to operate without a column oven then these boxes will be grayed out. Note: For the HP1100 a temperature should be entered in both the Left and Right boxes.
Stop Time	This value is set to the time in minutes that the method will run from the point of injection.
 Related Topics


Hewlett Packard Pump Gradient Timetable Page

This page allows a gradient to be entered and edited. To operate in isocratic mode ensure the timetable is empty.

To add a gradient, type in a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created.

The gradient parameters that you can set are as below. Note: The number of solvent percentages, which appear in the dialog, depends on which type of gradient was selected in the LC Configuration Window.

Time	The time at which you wish the following parameters to be attained during a method run.
%B	The percentage of solvent B you wish to attain at the given time.
%C	The percentage of solvent C you wish to attain at the given time.
%D	The percentage of solvent D you wish to attain at the given time.
Flow	The required flow in ml/min that you wish to attain at the given time.
Pressure	This is only available on the HP1050 and HP1100 and allows the limiting high pressure (in bars) to be reset at the given time.
 Related Topics


Hewlett Packard Pump External Events Page

External events allow control of the external contacts found on the HP1050 and HP1090 LC systems. In addition HP1090 column switching can also be controlled. For the HP1100 you must have the separate contact board installed in your pump in order to use this functionality.

The contacts can be set to operate under timed control during a method run, as well as having their initial states set. The contacts will be in the initial state before a method run and will return to this state after a method has completed.

To add events see the earlier section  Hewlett Packard Sampler External Events Page.

 Related Topics


Hewlett Packard 1100 G1367A Well Plate Autosampler

The Well Plate Autosampler has a number of additional features compared to older HP1100 autosamplers. These differences take the form of three new property pages, an additional menu and two new dialog boxes.

More:

Sampler Initial Conditions

Injector Parameters

Needle Wash

Configuration

Bed and Plate Layout


Sampler Initial Conditions

This page covers the basic variables for an injection and is common to all HP 1100 autosamplers all parameters are described in the" Hewlett Packard Sampler Configuration Page" section.

The maximum value for the Injection Volume depends on the values of the Seat Capillary Volume and the Syringe Volume (see Injector Parameters)

If the Seat Capillary Volume is greater than the Syringe Volume then the maximum Injection Volume is the Seat Capillary Volume plus the Syringe Volume (the autosampler supports multiple draws in this situation). Otherwise the maximum Injection Volume, is either half of the Loop Capillary volume or the Syringe Volume, whichever is smaller.

 Related Topics


Injector Parameters

Injection Procedure	Select from Standard Procedure, Injection With Needle Wash or Injector Program.
Volumes	Enter the Syringe, Seat Capillary and Loop Capillary Volumes. Only valid combinations of syringe, seat capillary and loop capillary volumes are allowed, which in turn specify min/max injection and draw speeds as shown below:
Product	Syringe (µl)	seat capillary (µl)	loop capillary (µl)	min. speed µl/min	max. draw speed µl/min	max. eject speed µl/min
µMonawell (standard)	8	0.3	8	1	20	100
µMonawell (optional)	40	0.3	80	1	250	250
Monawell (standard)	100	2.3	200	10	1000	1000
Monawell (optional)	100	400	200	10	1000	1000
Monawell (optional)	100	1400	200	10	1000	1000
Monawell (optional)	100	5000	200	10	1000	1000
Monawell (optional)	900	2.3	1800	90	1000	1000
Monawell (optional)	900	400	1800	90	1000	1000
High Throughput	Enable the Automatic Delay Volume Reduction by checking the box. Note: -The other options in this section box are currently not supported by MassLynx.
Timings	Enter an Equilibration Time and a Sample Flush Out Factor
 Related Topics


Needle Wash

Flush Port	Select the radio button to flush the port.
In Vial	Check the In Vial radio button to enable the In Vial edit box. Enter the number of the vial to wash.
Wash Time	Enter the time for the wash.
Repeat	Enter the number of time to repeat the wash.
 Related Topics


Agilent Systems - Hewlett Packard 1100 G1367A Well Plate Autosampler - Configuration
Configuration

This page selects and displays a schematic of the current bed layout for use with the method. To change the layout select a new one from the Tray Type drop down list.

 Related Topics


Bed and Plate Layout

One extra menu has been added for the Well Plate Autosampler - Beds and Plates.

Select Beds and Plates, Bed Layout to invoke the Bed Layout dialog. This dialog allows a given bed layout and appropriate plates be selected and saved.

 Related Topics

More:

Bed Layout Page

Edit Plates on Layout Page

Plate Generator


Bed Layout Page

This displays all the current bed layouts and allows them to be selected, which can then be edited on the Edit Plates on Layout page.

	Renames the selected bed layout
	Creates a new bed layout with the properties of the selected bed
	Deletes the selected bed layout. Note that it is not possible to delete the bed that is selected as the current configuration
	There are three default layouts ( One hundred vial tray, Two Trays and Two Well Plates plus 10 vials ) which can be renamed
 Related Topics


Edit Plates on Layout Page

This page allows individual plates to be selected on the bed layout, by clicking on the schematic.

Clicking on a plate will result in a Plate Select dialog box, containing the various plates allowed for the position chosen on that particular bed layout. In the case of the 100 vial plate and the 10 vial plate nothing will happen as these are the only valid plates for their default positions.

Clicking on a well plate will reveal the available choices, which can be configured:

Figure 3 The HP 1100 Well Plate Autosampler: - Edit Plates on Layout - Plate Select

Note: No Plate can now be selected as part of a valid bed layout configuration. Also the OpenLynx Login option is enabled

Clicking on a 15 vial plate or a 40 vial plate will result in the choices shown in Edit Plates on Layout Page Edit Plates on Layout Page:

Figure 4 The HP 1100 Well Plate Autosampler: - Edit Plates on Layout - Plate Select

The valid positions for the plates are summarized below.

Bed Layout	Positions	Valid Plates
One hundred vial tray	(1,1)	One hundred vial plate
Two trays	(1,1) and (2,1)	15 vials plate, 40 vials plate
Two well plates plus 10 vials	(1,1) and (1,2)	Agilent 96 Well Plate, Agilent 96 Deep Well Plate, Agilent 96 Capped Well Plate, Agilent 384 Well Plate. Also any user defined well plate
	(2,1)	10 vial plate
 Related Topics


Agilent Systems - Bed and Plate Layout - Plate Generator
Plate Generator

Selecting Bed Layout, Plate Generator invokes the Plate Generator dialog. At present, this only allows the plate information to be viewed and not changed.

 Related Topics


The HP Diode Array Detector

HP1050 PDA Detector

HP1100 DAD

HP 1050 UV Detector

Hewlett Packard 1090 UV Detector

HP 1100 UV Detector


HP1050 PDA Detector

Select View, HP1050 PDA Detector, Detector from the short cut bar or press the [image] toolbar button.

Range	Enter the minimum (Range) and maximum (To) wavelengths in nanometers over which diode array spectral data will be acquired.
Peak Width	Determines the rate at which the data is acquired. There are approximately eight spectra per peak so a peak width of 0.1 minutes means eight spectra will be acquired every 6 seconds.
Interval	This determines the number of spectral data points acquired. For example an interval of 4 nanometers means data points will be acquired at the lower wavelength, the lower wavelength plus 4nm and so on.
Autobalance	Check this box to zero the base line of the diode array detector before each analysis.
Use Pump Stop Time	Check this box to use the Stop Time defined on the Pump Initial Conditions page.
Stop Time	This option is not enabled if the Use Pump Stop Time box is checked. It determines the time in minutes the diode array method will run. Data will be acquired for this amount of time.
Save Data to Disk	Check this box to store the diode array data to disk. If you do not wish to save the diode array data to disk you should uncheck this box.
 Related Topics


HP1100 DAD

The HP1100 DAD dialog has Pre Autobalance and Post Autobalance in place of Autobalance. Check the relevant box to zero the baseline of the diode array detector before or after each analysis.

 Related Topics


HP 1050 UV Detector

Select View, HP1050 UV Detector, Detector from the short cut bar or press the [image] toolbar button.

Response	Select 250, 1000 or 4000 msec from the drop down list box.
Wavelength	Enter the wavelength in nanometers to be monitored.
 Related Topics


Hewlett Packard 1090 UV Detector

Select HP1090 UV Detector, Detector from the short cut bar or press the [image] toolbar button.

Response	Select one of the values from the drop down list.
Attenuation	Select one of the values from the drop down list.
Zero Percent	Increase the value to increase the baseline.
Filter Position	Set this to the number of the filter required.
Lamp Current	Set to Normal or High.
 Related Topics


HP 1100 UV Detector

Select HP1100 UV Detector, Detector from the short cut bar or press the [image] toolbar button.

Wavelength	Set to the wavelength in nanometers to be monitored.
Response	Select one of the values from the drop down list.
Zero Offset	Increase the value to increase the baseline.
Attenuation	Select one of the values from the drop down list.
 Related Topics


The HP6890 GC Control

System Status Page

HP6890 Sampler Configuration Page

HP6890 Injection Params Page

HP6890 Syringe Params Page

HP6890 Pump Setup

HP6890 Status Page

HP6890 Pressure Ramps Page

HP6890 Oven Page

HP6890 Oven Temp Ramps Page

HP6890 Post Run Page

HP6890 Front and Back Injector Pages

HP6890 Communication Parameters

The HP6890 Toolbar


System Status Page

The System Status page displays information about the state of the machine being controlled. This page can be accessed from the Inlet Editor by selecting Status from the View menu or by pressing the [image] toolbar button.

Indicators	The Running and Injector Cycle indicators at the left of the screen give information on the current status of the GC system. The OK and Ready Indicators become illuminated in red if the GC System has an error. Click on the red indicators to display more information on the cause of the error.
Run Time	This displays how long the method has been running.
Flow Rate	This is the current flow rate as returned by the instrument. The current value will be the setpoint when using a flow based mode or the actual flow if in a pressure based mode.
Pressure	This displays the current pressure in the instrument. The current value will be the setpoint when using a pressure based mode or the actual pressure if in a flow based mode.
Temperature	This displays the current oven temperature of the GC.
 Related Topics


HP6890 Sampler Configuration Page

Select View, HP6890 AutoSampler, Autosampler from the short cut bar or press the [image] toolbar button.

Fault	A red light indicates that the Autosampler has developed a fault.
Running	A green light indicates that the Autosampler is active. The Autosampler is active if it is moving a vial, rinsing or injecting.
Ready	A green light indicates that the Autosampler is ready to start processing another vial.
Autosampler Has Tray	Check this box if the Autosampler has a tray.
Autosampler Has Barcode Reader	Check this box if the Autosampler has a barcode reader.
Sample Number	Enter the vial number that the injection will be taken from, when the start button is pressed.
Start	Press this button to start an autosampler (and hence GC) run with the currently stored method.
Stop	Press this button to stop the Autosampler. It will not stop a GC run.
 Related Topics


HP6890 Injection Params Page

Injection Volume	Enter the injection volume to be used for a run started using the Start button on the Status and Connectivity page. Note: If the acquisition is started from the Sample List then this value will be overridden by the sample list injection volume.
Tray Temperature	This is used for record purposes only and is the tray temperature at which this method is normally used.
Solvent Washes	These allow a rinse strategy for each sample to be set up. Enter the number of washes of each type in the required boxes.
 Related Topics


HP6890 Syringe Params Page

Sample Pumps	Enter the number of times the syringe will draw in liquid in order to fill it.
Viscosity Delay	Select the length of time that the needle will stay in the vial to ensure that all the sample has been drawn into the syringe, from the drop down list box.
Slow Plunger	For viscous liquids select YES from the drop down list box otherwise select NO.
Allow Sampling Offset	Check this box to enable the Sampling Offset.
Sampling Offset	Enter the distance from the bottom of the vial (in millimeters) that the injection will be taken from. This is to allow samples to be taken from different parts of a multi-phased sample. Note: This box will bot be enabled unless the Allow Sampling Offset box is checked.
Pre Dwell Time and Post Dwell Time	If, for example the sample needs heating before injection, the syringe needle can be held in the GC inlet for Pre Dwell Time and/or Post Dwell Time. Enter the length of time in the relevant box.
 Related Topics


HP6890 Pump Setup

Select View, HP6890 Pump, Inlet from the short cut bar or press the [image] toolbar button.

 Related Topics


HP6890 Status Page

Prep Run	This will be yellow when the GC is in the Prep Run state. This occurs when the GC is trying to equilibrate before an automatic injection start.
Running	This will be yellow when the GC is in the Running state. This occurs when the GC has started its temperature and/or pressure profiles for a run.
Post Run	This will be yellow when the GC is in the Post Run state
Ready	This will be green when the GC is equilibrated and ready to start a run.
Error	This will be red when the GC is in an Error state or there is a communication problem between the GC and the Host (local PC).
Column 1 and Column 2	These boxes indicate the current status of the attached columns.
The Run Time, Current temperature, Current Pressure and Current Flow are described in the  System Status Page. Carrier Gas is described below.

 Related Topics

More:

HP6890 Column Page


HP6890 Column Page

There are two column settings pages, one for each column, both have the same functionality and are identical in appearance.

Length	Enter the column length in meters.
Internal Diameter	Enter the internal diameter of the column in micrometers.
Film Thickness	Enter the thickness of the column coating in micrometers.
Carrier Gas	Select a carrier gas from the drop down list box.
Injection Pressure Mode	Select Constant Pressure, Ramped Pressure, Constant Flow or Ramped Flow from the drop down list box.
Injection Port	Select Front or Back from the drop down list box.
 Related Topics


HP6890 Pressure Ramps Page

This appearance of this page will vary depending on the Injection Pressure Mode selected on the Column page. If Constant Pressure was selected only Initial Pressure and Initial Time are enabled. If Ramped Pressure was selected then the Ramps are enabled as well. If Constant Flow or Ramped Flow was selected, the parameters will be as for the corresponding Pressure page but Pressure will be replaced by Flow.

Initial Pressure/Flow	Enter the pressure/flow required for the Initial state.
Initial Time	Enter the length of time to remain at the initial pressure/flow
Ramps	To enable a Ramp check the relevant Ramp box or enter a non-zero value in the Rate box.
Rate	Enter rate of pressure/flow change for current ramp.
Temp	Enter final pressure/flow for current ramp.
Time	Enter the length of time to remain at the final pressure/flow of current ramp, before proceeding to the next ramp.
 Related Topics


HP6890 Oven Page

Max Oven Temp	Enter the maximum oven temperature. Temperatures entered in the ramps on the other pages will not be accepted if they exceed this parameter.
Equilibrium Time	Enter the time to wait at the Initial Temperature (defined on subsequent pages) before the ready signal is displayed.
Cryo cooling parameters	To enable these parameters check the Enabled box.
Cryo Uses CO2	Check this box if the cryo system uses CO2 instead of N2.
Blast Cooling Enabled	Check this box if the cryo system is to be used above ambient temperatures to speed up cooling of the oven.
Cryo Fault Enabled	Allows a fault to be generated on the GC if the Cryo system has been in continous operation for more than 16 minutes.
Cryo Timeout Enabled	Allows the cryo system to timeout and switch off the oven when the oven has been left ready at an equilibrated temperature for longer than the time enetered in the Cryo Timeout Time box
Ambient Temp	Enter the temperature regarded as normal ambient around the GC.
For a more detailed description of Cryo Fault & Timeout consult your HP6890 manual or site engineer.

 Related Topics


HP6890 Oven Temp Ramps Page

This window allows the oven temperature ramp profile for the GC run to be entered.

Initial Temperature	Enter the temperature required for the Initial State.
Initial Time	Enter the length of time to remain at the initial temperature.
Ramps	To enable a Ramp check the relevant Ramp No box or enter a non-zero value in the Rate box.
Rate	Enter rate of temperature change for current ramp.
Temp	Enter final temperature for current ramp.
Time	Enter the length of time to remain at the final temperature of the current ramp, before proceeding to the next ramp.
When setting Oven Temperature ramps the following points should be remembered: -

•	Any ramp will be used to ramp the temperature to the required temperature at the given rate.

•	The start time for the ramp will be the final time for the previous ramp.

•	Any ramp with a rate of zero will be the last ramp and will void any further ramps.

•	For an isothermal run, ramp 1 should be set to zero rate.

•	The final time for a ramp is the time at which the settings for that ramp become overtaken by those for the next ramp setting.

Illustration of Oven Ramp Settings


HP6890 Post Run Page

This appearance of this page will vary depending on the Injection Pressure Mode selected on the Column page. If Constant Pressure or Ramped Pressure was selected then a Post Run Pressure is required. If Constant Flow or Ramped Flow was selected then a Post Run Flow is required.

Post Run Enabled	Check this box if a Post Run is required.
Time	Enter the length of time for the post run phase.
Temp	Enter the temperature for the post run phase.
Pressure/Flow	Enter the head pressure/flow for the post run phase.
 Related Topics


HP6890 Front and Back Injector Pages

These two windows allow the type of inlet on the front and back slots to be selected. For all types other than "none" a configuration page is available that will be presented in the front or back inlet.

If none is selected in Injection Port Type there are no parameters to enter.

 Related Topics

More:

Cool on Column Inlet

Split/Splitless Inlet

Split Mode

Splitless Mode

Pulsed Temperature Vaporization (PTV) Inlet Page

PTV Settings Page

Split Mode (PTV)

Splitless Mode (PTV)

Pulsed Split Mode

Pulsed Splitless Mode

Solvent Vent Mode


Cool on Column Inlet

Figure 5 HP6890 Cool on Column Inlet: Ramped Temperature - Front Injector page.

Cool on Column	If Track Oven is selected, there are no parameters to enter.  If Ramped Temperature is selected, Cool on Column Inlet is displayed.
Thermal Zone On	Check this box to enable the Temperature, Time and Ramps fields. The Initial/Static conditions and Ramps details are used to provide a temperature profile for the inlet independent to the temperature profile of the oven, but the method of use is the same.
Initial Temperature	Enter the temperature required for the Initial State.
Initial Time	Enter the length of time to remain at the initial temperature.
Ramps	To enable a Ramp check the relevant Ramp box or enter a non-zero value in the Rate box.
Rate	Enter rate of temperature change for current ramp.
Final Temp	Enter final temperature for current ramp.
Time	Enter the length of time to remain at the final temperature of the current ramp, before proceeding to the next ramp.


Split/Splitless Inlet

If None is selected, there are no parameters to enter.

If Split is selected Split Mode is displayed.

 Related Topics


Split Mode

Figure 6 HP6890 Split Inlet - Front Injector page

Gas Saver Enabled	Check this box to save gas after an injection. The gas Flow and start time parameters are entered into the two edit boxes. • The gas saver flow must be at least 15ml/min greater than column flow. Note: Auto prep run must be manually set to ON if this box is checked. See the HP6890 manual for details.
Flow	Enter the reduced flow rate.
Time	Enter the length of time to deliver the reduced flow rate for.
Thermal Zone On	Check this box to enable the Temperature and Split Ratio fields.
Temperature	Enter the temperature at which to hold the inlet during the run.
Split Ratio	Enter the split ratio for the inlet flow.
 Related Topics


Splitless Mode

If Splitless is selected Splitless Mode is displayed.

Figure 7 HP6890 Splitless Inlet - Front Injector page

Gas Saver Enabled	Check this box to save gas after an injection. The gas Flow and start time parameters are entered into the two edit boxes. • The gas saver flow must be at least 15ml/min greater than column flow. • The gas saver start time should be after the purge time. Note: Auto prep run must be manually set to ON if this box is checked. See the HP6890 manual for details.
Flow	Enter the reduced flow rate.
Time	Enter the length of time to deliver the reduced flow rate for.
Thermal Zone On	Check this box to enable the Temperature, Purge Time and Purge Flow fields.
Temperature	Enter the temperature at which to hold the inlet during the run.
Purge Time	Enter the time at which to open the purge valve.
Purge Flow	Enter the flow rate to use at the Purge Time.
 Related Topics


Pulsed Temperature Vaporization (PTV) Inlet Page

Selecting a PTV mode on the front inlet creates a tabbable page for the PTV configuration. This page is removed should a non-PTV method be chosen.

Note: The back inlet cannot be fitted with a PTV.

There are five modes of operation on this inlet: Split, Splitless, Pulsed Split, Pulsed Splitless, and Solvent Vent. If None is selected, there are no parameters to enter.

Figure 8 HP6890 PTV Settings - Front Injector Page

PTV Cryo Parameters enabled	Allows the setting of the PTV cooling settings. If cooling is used, then the cryo method must be the same as that used on the oven.
Quick Cool	Check to enter the reduced flow rate.
Cryo Fault	Allows a fault to be generated on the GC if the cryo system has been in continuous operation longer than 16 minutes.
Cryo Timeout	Allows the cryo system to timeout and switch off the oven when the oven has been left ready at an equilibrated temperature for longer than the given time.
Cryo Method	Select from None, Air CO2 and N2.
Ambient Temp	Enter the ambient temperature. It has variable minimum values -160oC for liquid nitrogen, -60oC for liquid Carbon Dioxide and 5oC for compressed air. Iof no cooling is selected it will default to 24oC
 Related Topics


PTV Settings Page

Min Temp	The minimum temperature for all PTV injection port temperatures is based upon the cooling method. These values are described above for Ambient Temp.
Temperature Ramps	Each method on the PTV can have up to three temperature ramps. Time represents the hold time for the temperature once it has been reached.
 Related Topics


Split Mode (PTV)

Split operation is similar to that on the  Split/Splitless Inlet.

Figure 9 PTV Settings - Split Page

Gas Saver Enabled	Check this box to save gas after an injection. The gas Flow and start time parameters are entered into the two edit boxes. • The gas saver flow must be at least 15ml/min greater than column flow. Note: Auto prep run must be manually set to ON if this box is checked. See the HP6890 manual for details.
Split Ratio	Enter the split ratio for the inlet flow.
 Related Topics


Splitless Mode (PTV)

Splitless operation is similar to that on the  Split/Splitless Inlet.

•	Purge time and purge flow must be set.

•	Three temperature ramps can be set on the inlet

Figure 10 PTV Splitless parameters

 Related Topics


Pulsed Split Mode

This is similar to Split Mode (PTV) operation with the addition of pulsed pressure (Pulsed Split Mode ).

Figure 11 PTV Pulsed Split Parameters

Pulsed Pressure	Enter the pulsed pressure for the inlet valve.
Pulsed Time	Enter the pulsed time for the inlet valve.
 Related Topics


Pulsed Splitless Mode

This is similar to Splitless Mode but with the addition of pulse pressure and time set points.

Figure 12 PTV Pulsed Splitless Parameters

 Related Topics


Solvent Vent Mode

This mode requires several parameters to be set. Vent pressure and flow must be set, as well as the vent end time. These settings are for venting the solvent from the inlet, to concentrate the analyte. Purge flow and purge time must also be set.

Figure 13 PTV Solvent Vent Parameters

 Related Topics


HP6890 Communication Parameters

Select HP6890, View Comms Settings from the  Menu or press the [image] toolbar button to view the current communications settings.

Communication settings should only be changed by an engineer, the Edit Comms Settings and the [image] toolbar button allow this to be done.

 Related Topics


The HP6890 Toolbar

The HP6890 toolbar has five extra buttons on it, which are:

The HP6890 toolbar has five extra buttons on it, which are:

	View current communications settings.
	Edit current communications settings.
	Start and stop method.
	Turn GC on and off.
	Reset Autosampler
 Related Topics


Gilson Systems - Introduction
Introduction

Supported Models

Setting up

The Gilson Toolbar


Supported Models

The Gilson Software can be used to control any of these models:

Gilson 215	Gilson 231XL
Gilson 232XL	Gilson 233XL
Gilson 222XL	Gilson Quad-Z 215
The Gilson 232XL and 233XL also require the Gilson 402 Dilutor. The Gilson 401C Dilutor is also supported although this has now been discontinued by Gilson.

The Gilson 215 has a dilutor built in, but it does require a Gilson 819 Valve Actuator.


Setting up

The first time MassLynx is run with a Gilson Autosampler, it needs to know which autosampler is being used. The following dialog is displayed.

Figure 14 Gilson Defaults dialog

Select the installed Autosampler, Dilutor and Injector and press OK. Note: This need only be done the first time you use MassLynx or if the type of autosampler is changed.

Selecting a particular autosampler grays out unsupported combinations of modulus.

Valid combinations of modules are listed in the  Setting up .

Autosampler	Dilutor	Injector
Gilson 215	No Dilutor	No Injector Gilson 819 Gilson 889
Gilson 231XL or Gilson 232XL or Gilson 233XL	No Dilutor 401 C 402 Single Dilutor 402 Twin Dilutor 402 Duel Dilutor	No Injector
Gilson 222XL	No Dilutor	No Injector
Gilson Quad-Z 215	444 Quad Dilutor	Gilson 849 Gilson 889
Table 1 Valid Combinations of Gilson Modules

Once completed if a Gilson 215 or a Gilson Quad-Z 215 has been selected the following dialog is invoked:

Figure 15 Prompt dialog for Travel Height and Needle Height

Clicking Ok invokes the first property page of the Advanced Configuration dialog box described on 107. The travel and needle height values for the autosampler can be entered, although the defaults should be fine for most circumstances.

Note: - for the Quad-Z the travel height detected during the homing phase of the autosampler is used instead of the user-defined value if they are different.


The Gilson Toolbar

The Gilson toolbar has two extra buttons on it, which are:

	Prime the Dilutor.
	Generate Custom Racks.
 Related Topics


Gilson Configuration Pages

These pages contain information that is used to configure the autosampler. To access them press the [image] button, select Autosampler from the short cut bar or select View, Gilson AutoSampler.

More:

The Gilson Task List

The Individual Tasks (Gilson)

Gilson Dilutor Configuration Page

Gilson Sampler Configuration Page

Gilson Multi-Injector Parameters Page

Gilson Multi-Injector Processing

Gilson Advanced Options

The Gilson Bed Layout Editor

Modify Bed Layout (Gilson)

Adjusting The Arm Height on a Gilson 215 / Quad-Z 215

Other Advanced Options (Gilson)


The Gilson Task List

This page is used to build up a set of tasks into a method that is then used to perform the injection. The available tasks are contained in the Task drop down list box and the parameters displayed will depend on which task is selected.

For the Quad-Z 215 all options relating to left/right syringes and injector ports are not applicable and are grayed out.

 Related Topics

More:

Adding and Deleting Tasks (Gilson)

Modifying Tasks (Gilson)

Moving and Copying Tasks (Gilson)


Adding and Deleting Tasks (Gilson)

To add a task select it from the Task drop down list box, set the parameters and press the add [image] button. The task will be added to the end of the list.

To delete a single task, select it from the Task List and press the delete [image] button.

To clear all of the tasks in the Task List press the clear all [image] button.

 Related Topics


Modifying Tasks (Gilson)

To modify a task select it from the Task List, change the required parameters and press the add [image] button.

 Related Topics


Moving and Copying Tasks (Gilson)

To move a task, select it with the mouse, hold the mouse button down and move the task to the required position.

To copy a task follow the procedure for moving tasks but hold the CTRL key down when moving the mouse.

 Related Topics


The Individual Tasks (Gilson)

This section contains tables listing the individual parameters for each task.

More:

Inject Partial Loop

Detailed list of the steps that occur during the inject partial loop task.

Inject Total Loop

Rinse Injection Port

Rinse Inside Needle

Rinse Outside Needle

Set Electrical Contact

Wait For Contact

Wait For Time


Inject Partial Loop

This takes in the required values to perform a partial loop injection. In this method the injection volume plus an additional flush volume is aspirated. The Injection volume is entered in the sample list. The flush volume is defined in the  Gilson Dilutor Configuration Page.

Aspiration Flow Rate	The sample is drawn into the needle at this flow rate.
Displacement Flow	The sample is injected into the loop at this flow rate.
Valve Flush Volume.	This is the volume of solvent that is flushed through the valve after the injection. It is displaced at the Displacement flow.
 Related Topics


Detailed list of the steps that occur during the inject partial loop task.

Steps:

1.	Move to vial

2.	Aspirate air gap if required

3.	Move Z arm down to vial depth

4.	Aspirate injection volume + injection flush volume

5.	Move Z arm back to travel height

6.	Move to injection port

7.	Move to injection depth

8.	Switch valve to inject position

9.	Dispense injection flush volume

10.	Switch valve to load

11.	Dispense injection volume

12.	Switch valve to inject

13.	Pulse output contact

14.	Dispense air gap

15.	Rinse valve if a flush volume has been specified

Note: The Left and right valve become enabled when using a Gilson 233XL.

 Related Topics


Inject Total Loop

This is visually identical to inject partial loop. The difference being it does not make use of a flush volume, i.e. only the sample volume is injected. This function is now implemented for all Gilson autosamplers.

 Related Topics


Rinse Injection Port

This task is used to rinse the injection port with solvent from the reservoir.

Rinsing Volume	The volume of solvent that is rinsed through the needle.
Displacement Flow	The solvent is injected into the valve at this flow rate.
Note: The Left and right valve become enabled when using a Gilson 233XL.

 Related Topics


Rinse Inside Needle

This task is used to rinse the inside of the needle with solvent from the reservoir.

Rinsing Volume	This is the volume of solvent that is to be rinsed through the needle.
Displacement Flow	The solvent is rinsed through the needle at this flow rate.
Rinse Station	This is the rinse station at which you would like the rinse to take place. If this is set to auto then the nearest rinse station is chosen.
 Related Topics


Rinse Outside Needle

This task is used to rinse the outside of the needle with solvent from the reservoir.

Rinsing Volume	This is the volume of solvent that is to be rinsed through the needle.
Displacement Flow	The solvent is rinsed through the needle at this flow rate.
Depth	This is set to the depth that the needle should move to for rinsing.
Rinse Station	This is the rinse station at which you would like the rinse to take place. If this is set to auto then the nearest rinse station is chosen.
Because this task dispenses the solvent through the inside of the needle it also acts as a rinse inside needle.

Note: Rinsing the Outside of the needle is not available on the Gilson215.

 Related Topics


Set Electrical Contact

This task is used when you would like to set one of the output contacts.

Note. Different autosamplers have different numbers of contacts

Contact Number	This is the number of the contact that you would like to set.
State	This is the state that you want to set. Open, Close or Pulse.
 Related Topics


Wait For Contact

This task is used when you need to wait for a contact state.

Contact Number	This is the number of the contact that you would like to set.
State	This is the state that you want to set. Open, Close or Pulse.
 Related Topics


Wait For Time

This task is used if you need the machine to wait for a specified time.

Time	The time that you wish to wait for.
 Related Topics


Gilson Dilutor Configuration Page

This page is used to set parameters specific to the Dilutor. As already mentioned (in The Gilson Task List) when using a Quad-Z 215 there are no left/right syringe options, so there is just an option for All Syringes.

Syringe Volumes	The size of the currently installed Left and Right syringes.
Reservoir Aspiration Flow	This is the flow rate at which solvent is drawn from the reservoir (the default value is usually sufficient).
Prime Displacement Flow	This is the flow rate at which the solvent is displaced during the prime dilutor (the default value is usually sufficient).
Inlet Tubing volume	This is the volume of the tubing between the injection port and the rheodyne valve. It is the volume of air used to push the sample through into the injection loop.
Sample Flush volume	This is the amount of sample that is drawn with the injection valve. This amount is then injected before the valve switches to fill the tube between the valve and the injection port. Any excess will go to waste. Note: When using the Gilson 402 Dilutor, the Left and Right syringe radio buttons are enabled allowing you to use the left and right syringes. This is not yet available.
 Related Topics


Gilson Sampler Configuration Page

This page is used to set parameters specific to the Sampler. For the Quad-Z 215 the Rinse Station controls are grayed out.

Current Layout	Select the required layout from the drop down list box. A picture of the selected bed layout is displayed below the name.
Rinse Stations Present	Check the boxes if the rinse stations are present. Left and right are as you look at the machine. Note: When using the Gilson 215 the right rinse station will be disabled.
 Related Topics


Gilson Multi-Injector Parameters Page

This page is used to set parameters specific to the Gilson Multi-Injector System. This is an autosampler device that injects up to 8 samples simultaneously. The Multi-Injector itself consists of a Gilson 215 autosampler in conjunction with a Gilson 889 multi-valve injector. The device has eight needles connected to the robot arm and a syringe for each needle. The geometry of the autosampler is designed so that the 8 needles will enter 8 separate wells of a microtitre plate. The 8 samples are picked up at the same time and then deposited into 8 separate injection loops. The valves connected to these loops can then be controlled individually so that each of the samples can be sent to the mass spectrometer at any specified times.

To enable these parameters the following configuration must be defined.

1.	Select Advanced Configuration from the Gilson Sampler menu.

2.	On the Hardware tab select Gilson 215 from the Sampler drop down list box.

3.	On the Hardware tab select Gilson 889 from the Valve drop down list box.

4.	On the Hardware tab select All samples to same file from the Multi-Injector Mode drop down list box.

5.	On the Hardware tab check the Enable Inject Ahead box.

6.	Press OK.

Scan Time per Sample	This defines the analysis time spent on each sample.
Delay	This is the time for the sample to travel from the injection port to the mass spectrometer.
Length	This is the amount (in seconds) of the chromatogram that is used to create the data files for each of the samples
 Related Topics


Gilson Multi-Injector Processing

A complete row of 8 samples are collected simultaneously and placed in the injection ports. The injection valve for the first sample is switched to inject and a contact closure is used to signal the mass spectrometer to initiate scanning. Each subsequent sample is then injected every T seconds, where T is the Scan Time Per Sample defined on the multi-injector parameters page. Once all 8 samples have been injected the next set of samples are loaded in the injection loops. The first of these samples is injected after a time T from the last sample of the previous row.

The scanning time defined in the Mass Spectrometer method should be long enough so that all the samples can be injected and scanned. This time has to be calculated by the user.

Data for all samples is written to one file, the BatchDataFile, see below. Each peak within this chromatogram relates to a separate sample.

Figure 16 Multi-Injector Batch File

The file name of the BatchDataFile is based either on the sample list name or on the OpenLynx Job ID. A prefix of BATCH_ is added to this name so that it can be recognised as a BatchDataFile. E.g. for a sample list called Test.SPL, the name of the BatchDataFile will be BATCH_Test.RAW.

Once the scanning for the BatchDataFile is complete, ChroSplit.exe is used to create individual data files for each sample in the batch. ChroSplit.exe should be defined in the Acquire Process column for the first sample in the sample list or on the OpenLynx Setup Acquisition Process page.

ChroSplit reads the BatchDataFile.RAW and splits it into individual files based on the values defined on the Multi-Injector Parameters page. It ignores the first part of the file that is the Delay. The rest of the file is split into Scan Time per Sample sections and the scans acquired from the start of each of these sections for the defined Length are copied into the individual data files.

Figure 17 Multi-Injector Batch File

Some of the scans between any two samples will contain some mixing of samples (e.g. Region B) or not contain data relating to either sample (e.g. Region A). The data in these regions is not required, therefore only data in Length region is copied.

Once all data files have been created by ChroSplit the acquisition will proceed with any processing defined in the Process column for the first sample in the batch. For all subsequent samples in the batch no data is acquired only the processes are initiated.

ChroSplit currently writes two data files per sample. The first has a re-normalized retention time so that the retention time of the first scan for each sample is set to 0. This allows analysis of the masses to proceed via loop injection, which simply searches for masses contained within the scan at a user-defined retention time. The other file written retains its original retention time and is used to assess the accuracy of the ChroSplit procedure. This second data file has the prefix "CHECK_" added to the .RAW filename.

Figure 18 The results of using ChroSpilt.exe. Upper shows the Batch file, middle the re-normalized files and lower the check files

More:

Problems with ChroSplit


Problems with ChroSplit

If ChroSplit fails to copy the BatchDataFile scans correctly (due to an incorrect delay being defined or experimental faults, e.g. a change in pumping speed) then the delay and length parameters can be changed and the BatchDataFile reprocessed.

To do this the values in the timefile.tfl need to be changed. This file contains the time each sample reaches the mass spectrometer and is stored in the BatchDataFile.RAW directory. Also written to this file are the sample number, sample location for each sample and the multi-injector length and delay parameters.

[timefile]

MasterRawFile=Batch_xxxxx

Delay=4.5

Length=15

[Sample]  [Location]  [Injection Time]  [Sample ID]

1     "1,A" 	  0.195375 	   "Not used"

2     "1,B" 	  26.472376 	   "Not used"

3     "1,C" 	  46.591373 	   "Not used"

4     "1,D" 	  66.700378 	   "Not used"

Figure 19 Example timefile.tfl

1.	Open the timefile.tfl using a text editor, change the Delay or Length as required and save the file.

2.	Open the Sample List and change the Process for the first sample to ChroSplit.exe.

3.	Press the [image] button to display the Start Sample List Run dialog.

4.	Ensure that only the Auto Process Samples box is checked, the Run From Sample = 1 and the Run To Sample = 1, then press OK.

5.	This will split the BatchDataFile into the individual *.RAW files.

6.	On the Sample List change the Process back to the original processname and repeat step 3.

7.	Ensure that only the Auto Process Samples box is checked, the Run From Sample = 1 and the Run To Sample = last sample in the list, then press OK.

The data file for each sample will be recreated overwriting the previous files.

See the OpenLynx Users Guide, Introduction chapter for details on importing OpenLynx Batch files into the Sample List.


Gilson Advanced Options

Gilson Tray Options

Gilson Plate Generator

Creating and Deleting Plates (Gilson)

Default Plate Settings (Gilson

Rotating and Scaling Plates (Gilson)


Gilson Tray Options

To display the Tray Options dialog, select Options from the Gilson Tools menu on the Inlet Editor.

Colours	Select the colour to display the Selected vial, Non selected vial and Background from the appropriate drop down list box.
Display Gridreference on tray	Check this box to display the grid reference on the tray..
Gridreference text	From the drop down list box, select the colour in which you want the grid reference text to be displayed.
 Related Topics


Gilson Plate Generator

To display the Custom Rack Generator dialog, select Gilson Tools, Plate Generator or press the [image] button.

Rack Name	The name of the plate that is currently being edited.
Origin	The corner of the rack that the vial grid referencing starts from.
Rows	The number of vials in a row and the distance between each center.
Columns	The number of vials in a column and the distance between each center.
Vial	Diameter does not affect any parameters apart from how the tray looks in the Rack Generator. Depth affects how deep the needle travels into each vial when sampling. Decreasing the depth value will make the needle travel down further into the vial. This control is very important. An incorrect setting could send the needle through the bed and bend it.
Grid Reference	Allows the user to select the way that the vial rows and columns are referenced, e.g. whether the rows are alphabetical or numerical.
Referencing	This has three options  • XY which references the vials A1, B1 etc. • Sequential Discontinuous which numbers the vials 1, 2, 3 across a row, left to right, and then starts the next row from the left again. • Sequential Continuous which numbers the vials 1, 2, 3 across a row, left to right, then continues number the next row, right to left etc. If the Gilson autosampler is used with OpenLynx then the vial referencing must be set to either sequential continuous or sequential discontinuous..
Priority	Check the Horizontal First box if samples are to be acquired horizontally across the plate. If Referencing = X,Y, Horizontal = Letter, Vertical = Number and Horizontal Priority is checked, this will result in samples being acquired in the order A1, A2, A3. If the Horizontal Priority box is not checked samples will be acquired in the order 1A, 1B, 1C etc. If Referencing = sequential continuous or discontinuous and Horizontal Priority is checked, this will result in samples being acquired from row 1 then row 2. If the Horizontal Priority box is not checked samples will be acquired from column 1 then column 2 etc.
Offsets	Allows alternate vial rows or columns to be offset.
Plate Size	The size of the plate to its outside edges.
Top Left Vial Offset	The measurement to the center of the first vial from the top left corner of the plate.
 Related Topics


Creating and Deleting Plates (Gilson)

To create a new rack, press the [image] button. A new default rack is displayed, change the Rack Name, enter the appropriate values and press the save [image] button or select Save Current Rack from the Rack menu. New racks are saved to the MassLynx Plates directory.

To copy a custom rack, page through the list of saved custom racks using the [image] and [image] toolbar buttons.  The Previous Rack and Next Rack options on the Rack menu perform the same operation. When the required rack is displayed change the Rack Name, enter the appropriate values and press the save [image] button or select Save Current Rack from the Rack menu. New racks are saved to the MassLynx Plates directory.

To delete a custom rack select the rack to delete, by typing the name in the Rack Name box or by paging through as above, and press the delete [image] button or choose Delete Current Rack from the Rack menu.

Note: All of the spacings and the vial section are stored in 0.1mm units.

Note: When defining a custom plate for use with a multi-injector the plate is required to be compatible with the position of the 8 needles of the autosampler.

•	The Plate must have eight columns.

•	The position of the vials should allow all eight needles to enter a separate vial.

•	There should be no odd or even offsets for any of the vial positions.

 Related Topics


Default Plate Settings (Gilson

Selecting Default Settings for New Rack from the Tools menu displays the Default Settings dialog. This dialog allows the default settings used when creating a new rack to be defined. Field descriptions are the same as above.


Rotating and Scaling Plates (Gilson)

Selecting Rotate Rack from the View menu will rotate a rack by 90 degrees. For example:

Selecting Scale Rack from the View menu displays the following the Scale Rack dialog.

Move the slider or enter a new value to change the size of the rack as displayed in the Plate Generator dialog.


The Gilson Bed Layout Editor

To display the Bed Layout Editor dialog select Gilson Tools, Bed Layout Editor.

More:

To Create a New Bed Layout (Gilson)

To Delete a Bed Layout (Gilson)

To Create a New Bed Layout (Gilson)

Modifying the Number of Rows and Columns (Gilson)


Gilson Systems - The Gilson Bed Layout Editor - To Create a New Bed Layout (Gilson)
To Create a New Bed Layout (Gilson)

1.	Highlight a bed layout similar to the one you want to create and press the [image] button to create a new layout. The layout appears in the Bed Layouts list as the same name with a 1 at the end, e.g. Code 201 Bed Layout1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

New bed layouts are saved to the MassLynx Racks directory.

 Related Topics


To Delete a Bed Layout (Gilson)

Highlight a bed layout you wish to delete and press the [image] button. A dialog box will ask you to confirm the deletion. Press the OK button to delete the bed layout.

 Related Topics


Gilson Systems - The Gilson Bed Layout Editor - To Create a New Bed Layout (Gilson)
To Create a New Bed Layout (Gilson)

1.	Highlight a bed layout similar to the one you want to create and press the [image] button to create a new layout. The layout appears in the Bed Layouts list as the same name with a 1 at the end, e.g. Code 201 Bed Layout1.

2.	To change the name of the layout, type the new name into the Bed Layouts text box and press the [image] button. The name is updated in the Bed Layouts list box.

New bed layouts are saved to the MassLynx Racks directory.

 Related Topics


Modifying the Number of Rows and Columns (Gilson)

5.	To change the number of rows in the current column, type the new number into the Rows box and press the [image] button.

6.	To append a new column, press the [image] button.

7.	To delete the current column press the [image] button.

8.	To insert a column, click on the column before which you want to insert and press the [image] button. Note: The column inserted will have the same number of rows as the column highlighted.

 Related Topics


Modify Bed Layout (Gilson)

If the plate position or type needs changing, select the Modify Bed Layout tab.

9.	Click on one of the code plates to display the Plate Position and Type dialog.

This dialog allows you to select a new plate from a list of possible options, and change its actual position on the bed. Measurements for plate positions are always taken from the top left corner of each plate. The X value is the measurement from the currently selected plate to the plate immediately to the left. The Y value is the measurement from the currently selected plate to the plate immediately above. If there is no plate, to the left or above, then measurements are taken from the Home position, which is where the needle sits when not in use.

Rotated	Check this box if the plate is rotated.
OpenLynx plate login	If this box is checked and Use current MassLynx autosampler bed layout is checked in the OpenLynx Manager program, then the plate at this position can only be used for plate login on the OpenLynx Login program.
 Related Topics


Adjusting The Arm Height on a Gilson 215 / Quad-Z 215

The first time the Gilson software configuration pages are accessed the following dialog will be displayed. Type in the Needle Height that you have set the Gilson to and press OK.

For the Quad-Z 215 autosampler the Multi-Injector mode is always set to "Single Injection" and grayed out, and the "Enable Inject Ahead", "Injector and Collector", "Inject Contact 1" and "Inject Contact 2" are always grayed out.

 Related Topics


Other Advanced Options (Gilson)

The advanced options dialogs can be accessed by selecting Gilson Sampler, Advanced Configuration.

The parameters on these pages will be set up at installation and should not need changing.

 Related Topics

More:

Hardware Page

Positions Page

Communications Page


Hardware Page

This page defines the type of Gilson AutoSampler, Dilutor and Valve used. It also shows the state of the initial electrical contacts to the AutoSampler and pump, the pulse width and needle parameters.


Positions Page

The Positions page is configured differently, depending on which autosampler has been selected on the Hardware page. This page defines the integer position from the Home position of the needle, i.e. the position of the needle when not in use. It also defines the distances the needle needs to travel to the rinse stations.


Communications Page

This page defines the serial line communication between the Gilson and the PC.


Gilson Pump

The Gilson Pump pages can be accessed by selecting View, Gilson Pump, selecting Inlet from the short cut bar or by pressing the [image] toolbar button.

More:

Gilson Solvents and Flows Page

Gilson Gradient Timetable Page

Gilson Events Timetable Page

Gilson Pressures Page

Gilson Mixer Page

Pump Configuration


Gilson Solvents and Flows Page

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B, C, D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Solvent Name	Type in the solvent name.
Refill Time	This is the time required for the piston return stroke. Normally it is set to the lowest value (125ms). If cavitation or degassing occurs, then a higher value must be used. The minimum value is 125ms and the maximum 1000ms.
Compressibility	This is used to calculate a flow rate compensation for the compressibility of the solvent. See the Gilson User Guide for suitable values.
Run Time	This is the length of time, in minutes, the pump should run for
Flow Rate	This is the total flow rate of the solvent channels according to how you have configured the instrument.
 Related Topics


Gilson Gradient Timetable Page

This page allows a gradient to be entered and edited. To operate in isocratic mode ensure that the timetable is empty.

To add a gradient, type in a time, the required percentages and the flow rate, in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being created.

 Related Topics


Gilson Events Timetable Page

To add an event, enter a time, select an event from drop down box and press the [image] toolbar button.

To delete a single event, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being created.

 Related Topics


Gilson Pressures Page

To set pressure limits check the Manometric Module box and enter a Minimum and Maximum pressure.

The maximum pressure limit is determined by the smallest pump head size.

 Related Topics


Gilson Mixer Page

This page allows the mixing parameters to be changed for Gilson321/322 pumps. It will configure itself depending on the pumps selected in the  Pump Configuration.

 Related Topics


Pump Configuration

To change the number of pumps used select Pump Configuration from the Gilson Pump menu.

Select the number of pumps, the pump type, pump head and the GSIOC required.

 Related Topics


Gilson UV Detector

The Gilson UV Detector page can be accessed by selecting View, Gilson UV Detector, selecting Detector from the short cut bar or by pressing the [image] toolbar button. A single page of three editable parameters is displayed.

Wavelength (nm)	Enter the wavelength for monitoring..
Sensitivity (AU)	Enter the required sensitivity of the output signal.
Peak Width	Determines the rate at which the data is acquired. There are approximately eight spectra per peak so a peak width of 0.1 minutes means eight spectra will be acquired every 6 seconds.


Jasco 900 and Jasco 1500 Autosamplers

The Inlet Editor for the Jasco 900 and Jasco 1500 autosamplers is the same. The Jasco 900 is used in the following examples.

More:

Jasco Comms Setup

Jasco Sampler Initial Conditions Page


Jasco Comms Setup

It is possible to connect to the Jasco system using either the LC Net II ISA card or the newer ethernet enabled LC Net II Box. The default setting is to use the LC NetII ISA card. To change the communication setting, open up the Inlet Editor and select the Comms menu.

Selecting the ISA Net Card menu item simply configures the system to use the pre-installed Jasco drivers. If these are not present they must be installed.

Selecting the LC-NetII Ethernet menu item will open up a set of dialog boxes enabling you to configure the IP address of the LC-NetII Box (this must be connected for this operation to work ).

The first dialog allows you to set the IP address.

The second selects which system this IP address refers to.


Jasco Sampler Initial Conditions Page

This page is used to set parameters specific to the Sampler, to access it select View, Jasco900 AutoSampler, Autosampler from the short cut bar or press the [image] toolbar button.

Injection Volume	Enter the volume in microlitres to inject. Note: If a multisample acquisition is being run from the MassLynx Sample List, the injection volume defined in the sample list overrides the value defined here.
Flushes	Enter the number of times the needle should be flushed between injections.
Analysis Time	Enter the length of time the run will last..
Vial number	Enter the number of the vial to inject from. Note: If a multisample acquisition is being run from the MassLynx Sample List, the Bottle # entry in the sample list overrides the value given in the Vial Number entry above.
 Related Topics


Jasco 900 and Jasco 1500 Pumps

The Inlet Editor for the Jasco 900 and Jasco 1500 pumps is the same. The Jasco 900 is used in the following examples.

The Jasco Pump pages can be accessed by selecting View, Jasco900 Pump, Inlet from the short cut bar or by pressing the [image] toolbar button.

 Related Topics

More:

Jasco Initial Conditions Page

Jasco Gradient Page


Jasco Initial Conditions Page

Solvents	Up to three solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B and C	Check the box for the pump required and enter the percentage of flow to deliver from this pump. To disable the pump, uncheck the box.
Flow	This is the total flow rate of the solvent channels.
Mode	Select Isocratic (One pump), Binary (Two pumps), HPG (High Pressure Gradient) or LPG (Low Pressure Gradient).
Pressures	Enter the upper and lower limits of the pressure within the solvent delivery system (SDS), if the pressure falls outside of this range the SDS switches off.
Column Heater	If the instrument has an oven present then the column temperature can be set to a specified temperature in degrees centigrade. Check the Column Temperature box and enter a temperature. If the software has been configured to operate without a column oven then these boxes will be greyed out.
Stop Time	Enter the time in minutes that the method will run from the point of injection. If a Jasco Autosampler has also been selected, Analysis Time on the autosampler page overrides this value.
Post Time	Enter the time in minutes that the instrument will run in its initial conditions after a method has completed. No further injections can be carried out whilst the system is in post run thus allowing re-equilibration of the column.
 Related Topics


Jasco Gradient Page

This page allows a gradient to be entered and edited. If isocratic mode was selected on the Initial Conditions page then only relevant fields are displayed and no Gradient can be added to the Gradient Timetable. For other modes the relevant boxes (B% and C%)are enabled.

To add a gradient, enter a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient select the required entry in the timetable. The values will then be displayed in the edit boxes to the right of the timetable and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. Note: If the time is changed and the new time does not correspond with an existing entry in the table, then a new entry will be added. If the new time correspond to an existing entry then the entry at that time will be overwritten.

 Related Topics


Jasco 900 and Jasco 1500 UV Detectors

The Inlet Editor for the Jasco 900 and Jasco 1500 UV detectors is the same. The Jasco 900 is used in the following examples.

This page is used to set parameters specific to the UV detector, to access it select View, Jasco900 UV Detector, Detector from the short cut bar or press the [image] toolbar button.

Response	This can be set to Fast, Standard or Slow depending on the length of time you expect the peak to appear.
Wavelength	Set to the wavelength you want to monitor.
 Related Topics


Shimadzu Autosamplers

Shimadzu Autosampler Initial Conditions Page


Shimadzu Autosampler Initial Conditions Page

This page is used to set parameters specific to the Sampler, to access it select View, Shimadzu AutoSampler, select Autosampler from the shortcut menu, or press the [image] toolbar button..

Injection Volume	Enter the volume in microlitres to inject. Note: If you are running from the Sample List, the injection volume in the sample list entry overrides the setting used here.
Vial number	The vial to inject from. Note: If a multisample acquisition is being run from the MassLynx Sample List, the Bottle # entry in the sample list overrides the value given in the Vial Number entry above.
Rack Select	Select the type of rack required from the drop down list box.
Syringe Volume	Select the size of the currently installed syringe from the drop down list box.
Needle Stroke	Adjusts the depth of the needle tip to accommodate for sedimented samples or non-standard vials.
Rinse Volume	Enter the volume of solvent that is to be rinsed through the needle.
Rinsing Speed	Enter the speed at which the solvent is to be rinsed through the needle.
Sampling Speed	Enter the rate in microlitres per second at which sample is extracted into the autosampler needle. This should be set according to the viscosity of your sample.
Excess Volume	To ensure that the sample is not diluted with the rinse solvent more sample is drawn into the needle than will be injected. Enter the extra volume required.
Cooler Temperature	If the sample cooler is installed, enter the temperature that the sample should be cooled to.
MPT Tray	Select Dual or Single from the drop down list box.
 Related Topics

More:

To Set-up Communication Parameters (Shimadzu)


To Set-up Communication Parameters (Shimadzu)

Select Shimadzu, Configuration to display the Configuration dialog.

These parameters should be defined on setup and should only need changing if the Pump, Autosampler or mode of acquisition is changed. To change a value select a new one from the relevant drop down list box.

Pump Type	Choose from the list of Pumps
Mode	Choose from One Pump Isocratic, High Pressure Binary Gradient, High Pressure Ternary Gradient or a Low pressure Quaternary Gradient
Sampler Type	Choose from the list of Samplers
UV Detector	Choose from the list of Detectors.
Column Switching Valves.	Select the models of any column switching that are present and the ports on the options to which they are attached.
Deuterium Lamp Tungsten Lamp	Select either lamp The Tungsten Lamp is available for the SPD-10Avvp Pump and the Deuterium Lamp for SPD-10Avp Pump.
Column Switching Valves	Select which column switching valves to use.
Comunications	Select a Com Port and Baud rate
 Related Topics


Shimadzu Pump

The Shimadzu Pump pages can be accessed by selecting View, Shimadzu Pump on the Inlet Editor selecting Inlet from the short cut bar, or by pressing the [image] toolbar button.

More:

Shimadzu Initial Conditions Page

Shimadzu Gradient Timetable Page

Shimadzu Initial Events Page

Shimadzu Programmed Events Page


Shimadzu Initial Conditions Page

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B, C and D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Flow Rate	This is the total flow rate of the solvent channels according to how you have configured the instrument.
High Pressure Limit and Low Pressure Limit	Enter values as required. If the pressure falls outside these limits the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red.
Column Temperature Set	Enter the temperature to heat the column to. Note: This box will be greyed out if a column heater is not present.
Column Temperature High Limit	This is the maximum deviation in column temperature allowed. If this is exceeded the current acquisition will stop and the LC Status error light, on the MassLynx screen, will turn red.
Run Time	Enter the time in minutes that the method will run from the point of injection.
 Related Topics


Shimadzu Gradient Timetable Page

This page allows a gradient to be entered and edited. To operate in isocratic mode ensure that the timetable is empty.

To add a gradient, enter a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

To delete a single gradient click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created.

Flow	Enter the flow rate for the solvent delivery system.
Curve	This sets the rate at which the solvent is to change to the new proportions and/or flow rates. See the Shimadzu Operator's Guide for a list of values.
 Related Topics


Shimadzu Initial Events Page

This page allows the initial state of switches 1 to 4 to be defined.

Switch Events	Check the box(es) for the switches that should have an initial state of off.
Column Switches	Select the initial positions for column switches from the dropdown box.
 Related Topics


Shimadzu Programmed Events Page

This page allows the state of switches 1 to 4 and column switches A to D to be programmed.

To add an event, enter a time, select an event from the drop down list box, select an action (on or off) for normal switches or select a number from a drop down box for the column switches and press the [image] toolbar button.

To delete a single event, click a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify an event, select the required entry in the timetable. The values will then be displayed in the edit boxes above the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable, pressing [image] will result in a new entry being created.

 Related Topics


Shimadzu UV Detectors

This page is used to set parameters specific to the Sampler, to access it select View, Shimadzu UV Detector, select Detector from the short cut bar, or press the [image] toolbar button.

More:

Shimadzu UV Detector Page


Shimadzu UV Detector Page

Wavelength 1 Wavelength 2	Select between single and dual wavelength mode and enter the wavelength. Note. Depending on the UV detector used the valid range will be different.
Output Mode	Select from Ch2 O/P to Recorder, Ratio to Recorder or Ratio to Integration.
Ratio Range	Select and enter a ratio range. This only available when Ratio to Recorder or Ratio to Integration is selcted.
Ratio Threshold	Select and enter a ratio thrshold. This only available when Ratio to Recorder or Ratio to Integration is selcted.
Polarity	Enter a positive or negative polarity mode. This applies top both wavelengths.
Range	Enter a range in AUFS (Absorbance Unit Full Scale). The valid range is 0.00 - 2.56.


LC Packings - Introduction
Introduction

The UltiMate HPLC system consists of pumping units, UV detector and an autosampler. Optionally, users can configure the HPLC system with a Switchos. It is a switching unit that consists of two Valco 10 port low dispersion switching valves which allow for the connection of capillary, micro and nano HPLC columns. It is also attached to a high precision solvent loading pump, capable of separate flow rate from the main HPLC pump. There are two types of Famos autosampler, Famos Well Plate and Famos Carousel autosampler.

In addition, a menu is provided for incorporating into the Inlet Editor menu. All other functionality is provided by the Inlet Editor.

There are three separate views in the Inlet Editor, one each for the pump, UV detector and autosampler. Whether these are available or not depends on the configuration chosen in the Inlet Editor (see Chapter 1)


UltiMate Pump

The Ultimate Pump pages can be accessed by selecting View, Ultimate Pump from the Inlet Editor menu bar, Inlet from the short cut bar or by pressing the [image] toolbar button.

More:

Initial Conditions

Gradient

Initial Events

Configuration


Initial Conditions

Solvents	Up to four solvents will be displayed depending upon the system configuration. The total value of all the solvent percentages added together must not exceed 100%.
Pump A	This is the remainder percentage after the solvent percentages have been set for the other pumps.
Pump B, C and D	These can either be enabled or disabled by checking the box next to the individual pumps. The values can be set to the required percentage of flow delivery.
Solvent Name	Enter the name of the solvent that will be delivered through the corresponding Pump.
Flow Rate	This is the total flow rate of the solvent channels according to how you have configured the instrument.
Pressures	Enter the upper and lower limits of the pressure within the solvent delivery system (SDS) if the pressure falls outside of this range the SDS switches off.
Run Time	Enter the time in minutes that the method will run from the point of injection.
Hold Gradient	The Hold Gradient function is used to facilitate better peak separation. If the Hold Active box is checked, a Reduce Flow rate percentage can be entered to allow slower flow and gradient freeze. When a pulse/signal is generated by a mass spec or other scanning apparatus and received via contact closure at the back of the Pump (Start-In slot).
 Related Topics


Gradient

Note: The available inputs depend on the actual configuration.

This page allows a gradient to be entered and edited. Isocratic Binary, Ternary and Quarternary gradients can be formed when selected in the Initial Events page (page 121).

To enable the B%, C% and/or D% boxes check the relevant boxes on the Initial Conditions page.

To add a gradient, enter a time and percentage in the relevant boxes and press the [image] toolbar button. Note: The first entry must have a time of 0.

Enter Events from the Ev1 and Ev2 drop down boxes. If Switchos is present further event controls are enabled.

To delete a single gradient, click on a time in the list and press the [image] toolbar button.

To delete all entries press the [image] toolbar button. This button is only available when there are entries in the timetable.

To modify a gradient, select the required entry in the timetable. The values will then be displayed in the edit boxes to the left of the timetable, and can be altered as appropriate. Once changed press [image] to re-enter the values into the timetable. If, however, you modify the time value such that it does not correspond to any existing entry in the timetable pressing [image] will result in a new entry being created in the timetable.

B%	Pump B is not available in Isocratic mode and is grayed out when not enabled on the Initial Conditions page.
C%	Pump C is not available in Isocratic or Binary configuration mode and is grayed out when not enabled on the Initial Conditions page.
D%	Pump D is not available in Isocratic Binary or Ternary mode and is grayed out when not enabled on the Initial Conditions page.
Flow	Enter the flow rate for the solvent delivery system.
Loading Flow	This is only supported when Switchos is present. This flow is for the loading pump below the Switchos valves. When Switchos is present, four additional events are supported. Event 3 - Valve A Event 6 - Valve B Event 7 - SSV Event 8 - External Instrument
 Related Topics


Initial Events

This page allows the initial state of Events 1 to 8 to be defined. Select from the drop down lists On, Off, No Change or Pulse.

 Related Topics


LC Packings - UltiMate Pump - Configuration
Configuration

Selecting UltiMate, Configuration invokes the Configuration dialog allowing the user to change the configuration.

Gradient Mode	Choose from Isocratic, Binary Ternary or Quarternary.
Column Type	Choose from no column, ID 180ìm, ID 100ìm, ID 75ìm, ID50ìm.
Column Length	Choose from 5cm, 10cm, 15cm, 20cm, 25cm.
Stationary Phase	Choose from; GPC; C18, 5ìm 100A; C18, 3ìm, 100A; C18, 5ìm, 300A; C18, 3ìm, 300A.
Sampler Type	Choose from Famos Well Plate or Famos Carousel.
Mode	Check either Micro or Conventional.
Switchos	Check box to enable Switchos
Lamp	Indicates the Deuterium Lamp
UV Address	This unique instrument ID which can usually be found at the back of the instrument on a sliver label.
Pump Address	This unique instrument ID which can usually be found at the back of the instrument on a sliver label.
Sampler Device ID	This Device identifier can be found on the COMM. Page of the Famos display screen.
 Related Topics


Famos Autosampler

Autosampler Initial Conditions

Autosampler Method Configuration

Tray Configuration


Autosampler Initial Conditions

This page is used to set parameters specific to the Sampler, to access it select View, Famos AutoSampler, Autosampler from the short cut bar or press the [image] toolbar button.

Injection Volume	Enter the injection Volume between 0 - 100ìl
Flush Volume	Enter the volume of mobile phase required to flush the injector port after the sample has been injected. A value of zero will result in no flush. Enter a value between 0 - 999ìl.
Vial Reference	Enter the position of the vial to use for single sample acquisitions. For samples acquired via a sample list this is over ridden by the value in the sample list.
Loop Volume	Enter the Volume of the Loop between 5 - 1000ìl.
Needle Height	Enter a Needle Height.
Tubing Volume	Enter a tubing volume between 1ìl and 200ìl.
Syringe Volume	Select from 25ìl, 100ìl, 250ìl, 500ìl and 1000ìl. If the autosampler is in micro mode, the syringe size will be either 25ìl or 100ìl.
Syringe Speed	Select a Syringe speed from Low, Normal or High.
Rack Select	Select from 48-Vial, 96-Low, 96-Deep and 384 wells. If the autosampler is a Famos Carousel, the Rack Select option will disappear and the Tray Configuration option on the UltiMate menu is activated.
Injection Method	Select from ìl - pickup, Full Loop or Partial Loop
 Related Topics


Autosampler Method Configuration

Low Dispersion Method	This is only available if Micro mode has been selected in the Pump  Configuration. Check the L.D. Injection Method box and enter an L.D Factor.
Tray Cooling	To enable Tray Cooling, check the Tray Cooling box and enter a Tray Temperature.
Transport Vials	Enter the First and Last Transport Vials. If the sampler is of the carousel variety, the format of the Transport Vial will change from numeric to alphanumeric. Both the first and last transport vial have to be on the same vial segment. This option is only available if ìl - pickup method is selected.
Wash	Check the Wash after injection box and enter a Wash Volume.


Tray Configuration

If the autosampler selected on the Configuration dialog is a Famos Carousel the Tray Configuration is activated. This is invoked by selecting UltiMate, Tray Configuration.

Note. No combination of the segment type and number can be the same for any two segments.

 Related Topics


UV Detector

This page is used to set parameters specific to the UV Detector, to access it select View, Ultimate UV Detector, Detector from the short cut bar or press the [image] toolbar button

The UV Detector can operate in single or dual wavelength mode.

Wavelength 1	Enter the wavelength.
Wavelength 2	Check the box to enable Dual Wavelength mode and enter the wavelength
Full Signal Range	Select from the drop down box, 0.2, 0.5, 1.0, 2.0, 5.0 and 10.0.
Max Voltage Signal	Select from the drop down box, 0.2, 1 and 10.
Time Constant	Select from the drop down box, 0.2, 0.5, 1.0, 2.0, 5.0 and 10.0.
 Related Topics


CE Instruments GC8000 Gas Chromatograph

Note. CE Instruments are now only available on Transputer based instruments. Newer Non-Transputer based instruments no longer support these instruments.

On a CE Instruments GC8000, MassLynx can control the oven temperature, the injector zone temperatures, the valve times, the dump valve and 4 external event times.

More:

To change GC ParametersChromatograph

Changing Valve Event TimesChromatograph

To control the GC8000 DPFC optionChromatograph


To change GC ParametersChromatograph

1.	Choose Set up Inlet from the Acquisition Control Panel Instrument menu.

or -

Double click on the picture of the GC on the Acquisition Control Panel to display the GC8000 inlet editor shown below.

2.	Make any changes to the parameters. Note: The oven temperature ramp can be modified either by using the keyboard to enter times, temperatures and rates, or by dragging the small red handles on the graph with the mouse.

3.	Save the method using either Save or Save As from the File menu.

The time and temperature range of the oven temperature ramp can be controlled using the buttons displayed to the right of the ramp. Clicking on [image] will increase the range shown on the time axis. Clicking on [image] will increase the range shown on the temperature axis. Clicking on [image] alters the display ranges so that the oven temperature display fills the graph.

A full description of all the parameters in this editor is given in the GC8000 Series Instruction Manual.

 Related Topics


Changing Valve Event TimesChromatograph

Timed events such as Purge and Split times can be included in the GC method. These are programmed using the GC 8000 Valve Control editor shown below.

To display this dialog select Valve Timetable from the Valves menu. The events parameters are stored to disk when the GC parameters are saved, not when this dialog is closed so ensure that parameters are saved before starting an acquisition.

 Related Topics


To control the GC8000 DPFC optionChromatograph

MassLynx can control the DPFC option on the GC8000 for Quattro II and Platform instruments.

1.	Select Configuration from the GC8000 editor DPFC menu.

2.	Configure the left and right channels as required. Each channel can be set to flow, pressure or off.

3.	Select Left Channel or Right Channel from the GC8000 editor DPFC menu to load either the Flow Ramp or Pressure Ramp Editor depending how the channel is configured.

4.	Make any changes required and press OK to exit and save changes.

 Related Topics


CE Instruments AS800 Auto Injector

The CE Instruments AS800 Auto Injector can be used with the CE Instruments GC8000 gas chromatograph. The autosampler is programmed from MassLynx using the A200S editor. It is programmed in exactly the same way as the A200S system described above.

A full description of all the parameters in this editor is given in the AS800 Autosampler Instruction Manual.


CTC A200S Autosampler

These pages are used to set parameters specific to the Sampler, to access them select View, CTCA200S AutoSampler from the menu bar, Autosampler form the short cut bar or press the [image] toolbar button.

More:

CTC A200S Status Page

CTC A200S Parameters Page


CTC A200S Status Page

The Fault, Running and Ready indicators at the left side of the screen give information on the current status of the autosampler.

Indicator	Red	Green
Fault	Fault with the autosampler	No fault
Running	Not running	Running
Ready	Not ready	Ready
Vial	Enter the number of the vial to take the sample from, for a single injection. Note: When samples are acquired from the Sample List the number on the Sample List overrides this value. Press the [image] button to download the parameters to the LC system. Pressing the [image] button or choosing Load Method from the LC or CTC200 menu will perform the same action. Press the [image] button to run a single injection. Pressing the [image] button or choosing Run Method from the LC or CTC200 menu will perform the same action.
 Related Topics


CTC A200S Parameters Page

Sample Volume	Enter the volume of sample (in microlitres) to inject.
Air Volume	Enter the volume of air (in microlitres) to be drawn into the needle before the sample, to separate it from the previous sample.
Pull-up Volume	Enter the volume of sample (in microlitres) to draw into the needle for a sample wash.
Sample Washes	Enter the number of times to wash the needle with sample.
Solvent Washes Pre Injection	Enter the number of solvent washes to perform using solvent from reservoirs A and/or B, before an injection.
Solvent Washes Post Injection	Enter the number of solvent washes to perform using solvent from reservoirs A and/or B, after an injection.
Pull-up Count	Enter the number of times to pull up the Pull-up volume for a sample wash.
Pull-up Speed	Enter the speed (in microlitres per second) to pull up the Pull-up volume for a sample wash.
Pull-up Delay	Enter the time to wait between each pull up.
Injection Speed	Enter the speed (in microlitres per second) to inject the sample.
Pre Injection Delay	Enter the time to wait (in seconds) between the needle being injected and the plunger being depressed.
Pre Injection Delay	Enter the time to wait (in seconds) for the plunger to be drawn back after an injection
 Related Topics


CTC PAL Autosampler

Note: This is also labelled as the Waters 2777

These pages are used to set parameters specific to the Sampler, to access them select View, PAL_CC AutoSampler, Autosampler from the short cut bar or press the [image] toolbar button. When the autosampler parameters are selected, a warning message is displayed.

Note: For the Waters 2777 select View, Waters 2777.

When the software is installed a series of files are copied to the default.pro/Acqudb directory (*.pma, *.pol, and *.pmx).

When the autosampler page is selected the software looks for the presence of the PAL autosampler. If one is found information is read from the Latest_pal.pol file and Latest_pal.xml

 Related Topics

More:

PAL Cycle Composer Method Editor

Using the PAL CTC Autosampler with OpenLynx


PAL Cycle Composer Method Editor

You can only use a series of predefined methods which are listed as a drop down list in Available Cycles.

The parameters for each cycle are listed under Cycle Arguments. The value for each parameter can be edited.

The Method Editor contains the following buttons and fields:

Available Cycles	Lists all cycles available to the current instrument
Syringe	Sets the size of the installed syringe.
Description	Lets you enter a description of the current method.
Cycle Arguments	This table lets you define the value settings of each cycle argument of the selected cycle.
Default all	Replaces the entered values for each cycle argument with the default value.
 Related Topics

More:

Sample List Vial Referencing (CTC PAL)


Sample List Vial Referencing (CTC PAL)

For the CTC PAL autosampler the default Sample List vial referencing for a 96 well plate in Stack 1 is

 Stk1-01:1 to 96 for the first tray in stack 1

 Stk1-02:1 to 96 for the second tray in stack 1 etc.

I.e. Stk1-01:1 is entered in the SAMPLE_LOCATION (Bottle) column of the Sample List. To use the normal MassLynx referencing 1:1, 1:2, 2:1 etc. the trays have to be renamed. See page To Rename Trays (CTC PAL) for details.

Note: For OpenLynx the 1:1 tray:vial referencing must be used.

 Related Topics


Using the PAL CTC Autosampler with OpenLynx

When using the CTC PAL autosampler with OpenLynx the tray names must be defined numerically and in sequence.

Note: It is recommended that MassLynx is closed down whilst changes are made to the tray numbering. When MassLynx is restarted the changes will be picked up automatically.

 Related Topics

More:

To Rename Trays (CTC PAL)

Using Plates for OpenLynx Plate Login (CTC PAL)


To Rename Trays (CTC PAL)

Using the hand held controller, check the order of the tray holders.

Using the hand held controller, number the trays for the tray holders sequentially starting from 1.

E.g. if the tray holders are in the order:

Stack1

THldr1

Then the trays should be numbered starting at 1 for the first tray in stack 1 and continuing sequentially for THdr1 trays (see the example in below

To check that trays are numbered correctly select OpenLynx Plate Login from the Inlet Editor, Plate Login menu.

If the trays are correctly numbered then the dialog will appear as in Figure 10 If the numbering is incorrect i.e. trays for THdlr1 are numbered from 1 then the dialog will appear as in Figure 11.

Tray Holder	Tray Type	Default Tray Name	OpenLynx Tray Name
Stack1	MT96	Stk-01	1
Stack1	MT96	Stk-02	2
Stack1	MT96	Stk-03	3
Stack1	MT96	Stk-04	4
Stack1	MT96	Stk-05	5
Stack1	MT96	Stk-06	6
Stack1	MT96	Stk-07	7
Stack1	MT96	Stk-08	8
Stack1	MT96	Stk-09	9
Stack1	MT96	Stk-010	10
Stack1	MT96	Stk-011	11
Stack1	MT96	Stk-012	12
THldr1	VT98	THldr-01	13
THldr1	VT78	THdlr-02	14
Table 2 OpenLynx Tray Naming

Figure 20 OpenLynx Plate Login dialog

Figure 21 OpenLynx Plate Login dialog

 Related Topics


Using Plates for OpenLynx Plate Login (CTC PAL)

Select OpenLynx Plate Login from the Inlet Editor, Plate Login menu.

If a plate is labeled Disabled it can be used for single shot login. If a plate is labeled Enabled it can be used for plate login. To change the state double click on the tray number.

 Related Topics


Cetac ASX100 Autosampler

Technical details of this autosampler are to be found in the manual supplied with the Cetac ASX 100 autosampler.

Vial Number	Enter the number of the vial to take the sample from. Note: When samples are acquired from the Sample List the number on the Sample List overrides this value.
Standard Tube	Check this box if standard vials are being used. The rack codes section will be grayed out and vial number can only be 2 to 14.
Uptake Time	Enter the time in seconds for the sample to travel from the sample vial to the Mass Spectrometer.
Before Sample	Check this box to rinse the needle before each sample.
Rinse Time	Enter the time in seconds required to rinse the needle.
Rack Codes	Click on the code required for the rack.


Cetac ASX500 Autosampler

Technical details of this autosampler are to be found in the manual supplied with the Cetac ASX 500 autosampler.

Vial Number	Enter the number of the vial to take the sample from. Note: When samples are acquired from the Sample List the number on the Sample List overrides this value.
Standard Tube	Check this box if standard tubing is being used. The rack codes section will be grayed out and vial number can only be 1 to 10.
Sipper Depth	Enter the depth in millimeters the needle should travel to. Note: The default probe sampling depth is measured from the neck of the tube to the tip of the probe.
Uptake Time	Enter the time in seconds for the sample to travel from the tubing to the Mass Spectrometer
Rack Codes	Click on the code required for each rack.
Rinse Before Sample	Check this box to rinse the needle before each sample.
Rinse Time	Enter the time in seconds required to rinse the needle.


Solids Probe

The temperature of a solids probe can be controlled during an acquisition. To do this you must set a ramp that defines the temperature of the probe tip against retention time. The ramp can have up to 5 'segments' which each have a start temperature, a time for which the probe will be held at that temperature, and a rate at which the probe will be heated to reach the start temperature of the next ramp segment (if there is one).

In addition to these controls, TIC (Total Ion Current) control of the probe is also available. If TIC control is selected then the TIC value is monitored during the acquisition and that information is used to modify the programmed ramp in such a way that the system attempts to keep the TIC at or below the 'Maximum TIC' value. This feature is very useful as it stops samples from being 'burnt off' the probe prematurely.

The actual temperature ramp used can be stored with the data file and a remote contact closure can be used to start the ramp. The External Contact Start box should be checked when a robotic probe system is being used.

More:

To Change probe control parameters (Solids Probe)

Programming the Temperature Ramp (Solids Probe)

Using TIC Control (Solids Probe)


To Change probe control parameters (Solids Probe)

1.	Choose Methods, Inlet from the Acquisition Control Panel  menu

-or-

Double click on the probe icon on the Acquisition Control Panel to bring up the solids probe editor shown below.

2.	Make any changes to the parameters.

3.	Save the method using either Save or Save As from the File menu.


Programming the Temperature Ramp (Solids Probe)

The probe temperature ramp can be programmed using the keyboard or by dragging the small red handles on the picture of the ramp itself.


Using TIC Control (Solids Probe)

To use the TIC control feature you must first check the TIC Control box, which will enable the values in the TIC control group to be modified. There are 3 values that you then need to set.

Minimum	Sets the value for the TIC above which the probe ramping is reduced. If the actual TIC seen from the instrument is below this value, the full heating rate, as programmed into the temperature ramp is used to heat the probe. As the TIC rises above this value, the heating rate is linearly adjusted down based on the difference between this minimum value and the maximum value discussed next. For example, a TIC value exactly between the maximum and minimum values would give a 50% rate compared to that requested by the ramp parameters.
Maximum	Sets the value for the TIC at which the probe ramping is suspended. This is done because the system is trying to keep the TIC at this level and further heating would cause it to rise above it. If the TIC reaches this level, heating will not recommence until it falls back down below
Finish	Sets a value for the TIC below which the acquisition of data will terminate. The temperature program will continue however to allow any remaining sample to be burnt off.


DCI Probe

A DCI probe can be controlled in the same way as a solids probe, as described above with the exception that the ramp is programmed for Current rather than temperature and the DCI current can be stored with the data file, not the probe temperature.


Thermospray Probe

A thermospray probe can be controlled in the same way as a solids probe, as described above, with the exception that the thermospray nozzle temperature can be stored instead of the probe temperature.


RoboProbe

A robotic probe system can be used in conjunction with a CE Instruments A200S auto injector, or a Zymark laboratory robot.

More:

CE Instruments A200S

Zymark Labmate


CE Instruments A200S

If the A200S is used then setting it up is done as described earlier.


Zymark Labmate

The Zymark setup editor allows you to select a solvent for your sample.

1.	Choose Methods, Inlet from the Acquisition Control Panel  menu

or

Double click on the Picture of the auto injector on the Acquisition Control Panel to bring up the Zymark editor shown below.

2.	Make any changes to the parameters.

10.	Save the method using either Save or Save As... from the File menu.


Contact Closure

Contact closure is a common method of providing start/stop control of an external inlet system. Many chromatographs, both LC and GC support contact closure because it is often used to provide control of an integrator unit. MassLynx uses essentially the same method of synchronization for acquiring data, the mass spectrometer's control unit using the start and stop signals produced by the chromatography system to start and stop data acquisition


Glossary of Terms

GSIOC ID

MUX


GSIOC ID

Gilson Serial Input Output Channel


MUX

MUX-technology™ allows 4 sample streams to be multiplexed (MUX) with one orthogonal acceleration Time-Of-Flight (oa-TOF) MS detector