EASY-nLC Series Xcalibur Data System 2.1 or Later User Guide

EASY-nLC Series Xcalibur Data System 2.1 or Later User Guide

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Setting Up the Foundation Instrument Configuration

This chapter describes how to set up the instrument configuration for the EASY-nLC device driver.

Before you set up the instrument configuration, connect the EASY-nLC instrument to the data system computer, turn on the EASY-nLC instrument, and log in to the instrument as an administrator. Then, use the Thermo EASY-nLC Configuration dialog box of the Thermo

Foundation Instrument Configuration window to set up and test the network connection for the EASY-nLC instrument, to specify the tray type that you plan to use, and to identify the mobile phase solvents in solvent reservoir bottles A and B.

Contents

Connecting the EASY-nLC Instrument to the Data System Computer

Adding the System Devices to the Instrument Configuration

Setting Up the EASY-nLC Configuration

Setting Up the Sample Layout and Start Position

Connecting the EASY-nLC Instrument to the Data System Computer

The EASY-nLC instrument and the Thermo Scientific mass spectrometer communicate with the data system computer through an Ethernet connection routed through an Ethernet switch connected to the data system computer.

These are the default IP addresses of the data system computer and the EASY-nLC instrument.

Table 3. Default IP addresses for the LC system

System module

Data system computer

EASY-nLC instrument

IP address

172.16.0.101

172.16.0.103

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Setting Up the Foundation Instrument Configuration

Adding the System Devices to the Instrument Configuration

To connect the EASY-nLC instrument to the data system computer

1. Connect a shielded Ethernet cable to the LAN port on the back panel of the EASY-nLC instrument.

2. Connect the other end of the Ethernet cable to an Ethernet switch.

3. Using a second shielded Ethernet cable, connect the Ethernet switch to the appropriate network card installed in the data system computer.

For more information about setting up the communication cables, refer to the EASY-nLC

Series Getting Started Guide.

IMPORTANT Avoid IP conflicts with other units on the network, especially the mass spectrometer.

Adding the System Devices to the Instrument Configuration

Your Thermo Scientific LC/MS system consists of a Thermo Scientific mass spectrometer and an EASY-nLC instrument. To control these instruments from the Xcalibur data system, you must add the installed device drivers to the instrument configuration.

Note The Xcalibur data system and the Foundation Instrument Configuration window cannot be open simultaneously.

To add devices to the instrument configuration

1. Close the Xcalibur data system if it is open.

2. From the Windows taskbar, choose Start > Programs (or All Programs) >

Thermo Foundation x.x > Instrument Configuration, where x.x is the installed version of Thermo Foundation.

The Thermo Foundation Instrument Configuration window opens (see

Figure 4

). The installed devices are listed in the Available Devices list. The configured devices are listed in the Configured Devices list.

Figure 4

shows an instrument configuration with a Thermo Scientific mass spectrometer added to the Configured Devices list.

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Setting Up the Foundation Instrument Configuration

Adding the System Devices to the Instrument Configuration

Figure 4.

Thermo Foundation Instrument Configuration window

Thermo Scientific

Tip To access Help, press F1 or click Help.

3. Add the EASY-nLC instrument to the instrument configuration as follows: a. Make sure that the Device Types list is set to All or AS (Autosampler).

If the Device Type list is set to LC, the EASY-nLC VI for Xcalibur device does not appear in the Available Devices list.

b. In the Available Devices list, double-click the Thermo EASY-nLC icon.

A copy of the Thermo EASY-nLC icon appears in the Configured Devices list.

4. Set up the configuration options for each configured device.

For information about the EASY-nLC configuration parameters, see the next topic,

“Setting Up the EASY-nLC Configuration.”

5. Click Done to close the Thermo Foundation Instrument Configuration window.

Tip You must close the Instrument Configuration window before you open the

Xcalibur data system. The two applications cannot be open at the same time.

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

Setting Up the EASY-nLC Configuration

Use the Thermo EASY-nLC Configuration dialog box to set up and test the communication connection to the data system computer, to specify the autosampler model and the plate type that you are using, and to identify the mobile phase solvents. Clicking the Edit button in the

Autosampler Configuration area opens the Sample Position Selector dialog box where you set up the sample layout (row first or column first) and the start position for an Xcalibur injection sequence.

To set up the EASY-nLC configuration in the Foundation platform

1. If you have not already added the EASY-nLC instrument to the Configured Devices list of the Thermo Foundation Instrument Configuration window, add it as described in

“Adding the System Devices to the Instrument Configuration” on page 8 .

2. In the Configured Devices list of the Thermo Foundation Instrument Configuration window, double-click the Thermo EASY-nLC icon.

The Thermo EASY-nLC Configuration dialog box opens (see Figure 5 ).

Figure 5.

Thermo EASY-nLC Configuration dialog box

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Thermo Scientific

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

3. Ensure the following:

• The EASY-nLC instrument is connected to the data system computer by way of an

Ethernet switch (see

“To connect the EASY-nLC instrument to the data system computer” on page 8 ).

• The EASY-nLC instrument is turned on, and you are logged in as an administrator to the instrument.

4. Set up the network configuration for the EASY-nLC instrument as follows: a. Type the IP address of the EASY-nLC instrument and your user name in the appropriate boxes.

You must have an account on the EASY-nLC instrument with the same user name.

The default user name is “admin,” but you can change this to any existing user account on the EASY-nLC instrument.

Tip The EASY-nLC IP address is listed in the About box, which you can open by pressing the THERMO logo in the upper-left corner of the touch screen. The current user is listed in the lower-left corner of the touch screen.

If necessary, change the IP address on the Configuration > Network page of the touch-screen software. b. Click Test Connection to test the connection to the EASY-nLC instrument and to download the instrument configuration information to the data system computer.

5. Check the message in the status box to the right of the Test Connection button.

• If the connection is established, the status box changes to green (see

Figure 6

) and the information about the LC device driver and instrument appears.

• If a connection is not established, the status bar changes to red. Check the Ethernet cable connections, the IP address of the EASY-nLC instrument, and the IP address of the network card installed in the data system computer (see

“Connecting the

EASY-nLC Instrument to the Data System Computer” on page 7 ).

• If an antivirus program or firewall blocks the connection, the application displays this error message:

An established connection was aborted by the software in your host machine.

Contact your local IT administrator for assistance.

For information about excluding the EASY-nLC software from the McAfee virus scanner, see

“Excluding the EASY-nLC from the VirusScan Enterprise” on page 5 .

6. Check the instrument information. If necessary, change the instrument information as described in

“To change the loop volume, column setup, idle mixture, or idle flow rate” on page 13

.

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

7. Set up the autosampler configuration in the Autosampler Configuration area as follows: a. Select the autosampler model (Autosampler ASA or Autosampler ASC).

b. Select the plate type (96- or 384-well plates, or a 4 × 6 (ASA) or 6 × 8 (ASC) vial holder).

Note All plate formats for the ASC model have six extra vial positions on the side. When you set up an Xcalibur sequence, these vials are numbered

1-V1 to 1-V6.

Figure 6.

Thermo EASY-nLC Configuration dialog box

Touch-screen software version 3.1

Edit button c.

(Optional) Set up the default sample layout and start position to be used when

creating a new Xcalibur sequence as described in “Setting Up the Sample Layout and

Start Position” on page 17 .

8. In the Solvents for LC Pump area, type the names of the solvents in the boxes for solvent bottles A and B.

Solvent bottle A typically contains LC/MS-grade water with 0.1% formic acid. Solvent bottle B typically contains LC/MS-grade acetonitrile with 0.1% formic acid.

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

9. If the OK button is unavailable, click Test Connection to download the new configuration settings to the data system computer.

10. Click OK to accept the settings and close the Thermo EASY-nLC Configuration dialog box.

11. Click Done to close the Thermo Foundation Instrument Configuration window.

You must close the Foundation application before opening the Xcalibur data system. The

Xcalibur data system and the Thermo Foundation Instrument Configuration window cannot be open at the same time.

To change the loop volume, column setup, idle mixture, or idle flow rate

1. From the instrument’s touch screen, do the following: a. Open the Maintenance > Devices page.

b. In the Devices list, select EASY-nLC (HPLC), and then press the Properties tab.

The Properties view for the HPLC device on the Maintenance > Devices page opens

( Figure 7 ).

Figure 7.

EASY-nLC (HPLC) properties view (touch-screen software version 3.0 or later)

Thermo Scientific c.

Press the corresponding box to open the keypad and enter the appropriate numeric values for these parameters:

• For Loop Volume, type the nominal volume of the sample loop installed on valve S (5, 20, or 50 μL).

• For Idle Flow Rate, type an appropriate value, in nL/min. When idle, the instrument pumps the specified solvent mixture at the specified flow rate.

• For Idle Mixture %B, type a value from 0 to 100.

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration d. Select or clear these check boxes as appropriate: One Column Setup and Load Speed

Protection (LSP).

Note The LSP check box is available in the 3.0 or later version of the EASY-nLC touch-screen software.

e.

Click Apply.

2. In the EASY-nLC Configuration dialog box of the Foundation Instrument Configuration window, click Test Connection. Then verify the new settings.

EASY-nLC Configuration Dialog Box Parameters

When you establish a connection between the EASY-nLC instrument and the data system computer, this dialog box displays the user-specified loop volume, idle flow rate, idle mixture, and column setup. You set these parameters from the EASY-nLC touch-screen software as

described above in “To change the loop volume, column setup, idle mixture, or idle flow rate.”

Table 4 describes the parameters in the Thermo EASY-nLC Configuration dialog box.

Table 4. EASY-nLC Configuration dialog box parameters (Sheet 1 of 3)

Parameter Description

EASY-nLC Network Configuration

Use this area to specify the IP address for the EASY-nLC instrument.

IP Address/Hostname Specifies the IP address of the EASY-nLC instrument. This value must match the value stored by the instrument.

User Name

Tip To check the IP address and host name stored by the instrument, press the company logo in the upper-left corner of the EASY-nLC touch screen.

Specifies the user name.

Note The user name that you type in this box must match the user name for the person currently logged in to the instrument. The user name is listed in the lower-left corner of the EASY-nLC touch screen. For information about logging in to the EASY-nLC instrument, refer to the EASY-nLC Series Getting Started Guide.

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Setting Up the Foundation Instrument Configuration

Setting Up the EASY-nLC Configuration

Table 4. EASY-nLC Configuration dialog box parameters (Sheet 2 of 3)

Parameter

Test Connection button

Description

Tests the Ethernet connection between the data system computer and the EASY-nLC instrument. If the connection is established, the status box to the right of the button turns green and contains this message: Connection OK.

In addition, the LC device driver and instrument information appears in the box below the status bar.

IMPORTANT If the following message appears, exclude the Thermo EASY-nLC

software from the McAfee virus scanner as described in “Excluding the EASY-nLC from the VirusScan Enterprise” on page 5

:

An established connection was aborted by the software in your host machine.

Contact your local IT administrator for assistance.

LC Device Driver and Instrument Information

LC Device Driver

LC Instrument

Driver Info

Serial Number

Loop Volume

Idle Flow Rate

Displays the LC device driver version.

Displays the instrument type.

Displays the instrument’s touch-screen software version.

Displays the serial number that is listed on the instrument’s back panel.

Displays the user-specified loop volume stored by the EASY-nLC instrument.

Displays the user-specified idle flow rate that the instrument maintains at the end of an injection sequence.

Idle Mixture

Entering a value of 0 deactivates this feature.

Tip Maintaining long-term emitter stability (with glass emitters) might require a constant solvent flow through the system.

Displays the user-specified solvent composition (%B) that the instrument is to pump through the system at the end of an injection sequence.

Column Setup

IFC

Displays the user-specified selection. Displays One Column or Two Column.

Displays whether the intelligent flow control (IFC™) mode is enabled. The IFC mode is a user-selectable option in the touch-screen software version 2.8.

Max Pressure

Autosampler Configuration

Displays the maximum system pressure.

Use this area to select the autosampler type, plate type, sample layout, and initial vial position.

Autosampler Specifies the autosampler model:

• ASC—Autosampler with refrigerated compartment and 6 extra vials

• ASA—Autosampler with a cooled plate and without the 6 extra vials

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Setting Up the EASY-nLC Configuration

Table 4. EASY-nLC Configuration dialog box parameters (Sheet 3 of 3)

Parameter

Plate Installed

Sample Layout

Start Position

Edit button

Description

Specifies the plate type that you plan to use: 96 well plate, 384 well plate, or 6 × 8 vial plate.

Displays the default sample layout (vial or microplate well positions) for an injection sequence.

Displays the default initial sample position for an injection sequence.

Opens the Sample Position Selector dialog box where you can select the sample layout and

initial position for an Xcalibur sequence (see “Setting Up the Sample Layout and Start

Position” on page 17 ).

Solvents for LC Pump

Use this area to describe the solvents that make up the gradient.

A

B

Specifies the solvent in solvent bottle A.

Specifies the solvent in solvent bottle B.

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Setting Up the Foundation Instrument Configuration

Setting Up the Sample Layout and Start Position

Setting Up the Sample Layout and Start Position

When you open the Sample Position Selector dialog box from the Thermo EASY-nLC

Configuration dialog box, the Number of Samples to Select box and the Select button are unavailable.

When setting up the configuration options for the EASY-nLC instrument, use the Sample

Position Selector dialog box to set up the sample layout and initial vial or microplate well position for an injection sequence.

For information about using the Sample Position Selector dialog box to interactively select the

vial or microplate well positions for an injection sequence, see “Setting Up the Injection

Positions with the Sample Position Selector” on page 41

.

To set up the sample layout and start position for an Xcalibur injection sequence

1. In the Autosampler Configuration area, click Edit.

The Thermo EASY-nLC Sample Position Selector dialog box opens. The Number of

Samples to Select box is unavailable (see Figure 8 ).

Figure 8.

Sample Position Selector dialog box

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Setting Up the Foundation Instrument Configuration

Setting Up the Sample Layout and Start Position

2. In the Sample Positions area, click Clear All.

3. In the Plate Rack area, select the default initial sample position by clicking a position.

4. In the Sample Selection Layout area, select the Row First or Column First option.

5. Click OK to save your changes and exit the Thermo EASY-nLC Sample Position Selector dialog box.

Note You can also open the Thermo EASY-nLC Sample Position Selector dialog box by clicking Select Vials in the Samples area of the Xcalibur New Sequence Template

dialog box (see Figure 13 on page 37

).

Sample Position Selector Dialog Box Parameters

Table 5 describes the parameters in the Sample Position Selector dialog box. When you access

this dialog box from the EASY-nLC Configuration dialog box, only the Sample Position

Layout and Initial Position parameters are available.

Table 5. Sample Position Selector dialog box parameters (Sheet 1 of 2)

Parameter

Plate Rack

Description

Use this area to select or clear the sample positions.

Vial Rack

For an EASY-nLC instrument with an ASC model autosampler (standard in the EASY-nLC 1000 instrument), you can select or clear a sample position from the additional 6 vials.

Note The additional vials are located on rack 1 and are called 1-V1 to 1-V6.

Sample Selection Layout

Row First

Column First

When you select the Row First option, the data system fills the sequence table with the sample positions row by row.

When you select the Column First option, the data system fills the sequence table with the sample positions column by column.

Note The sequence editor ignores the Sample Selection Layout option when you select the vial or well positions by clicking a set of samples in the Plate and Vial Rack areas.

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Setting Up the Foundation Instrument Configuration

Setting Up the Sample Layout and Start Position

Table 5. Sample Position Selector dialog box parameters (Sheet 2 of 2)

Parameter Description

Sample Positions (click on plate)

Initial Position

Number of Samples to

Select

Clear All button

Select button

Specifies the first vial or microplate well position in the sequence table.

Specifies the number of samples to add to the sequence table in addition to the initial vial position.

Clears all of the Plate and Vial Rack entries and the Initial Position entry.

Sequentially selects the number of vial or well positions specified in the Number of Samples to Select box. The selected vials or wells are highlighted in green in the Plate Rack and Vial

Rack areas. The vials or wells are ordered sequentially according to the sample selection layout selection.

Dialog box buttons

OK

Cancel

Accepts the settings and closes the dialog box.

Closes the dialog box without accepting the changes.

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