EASY-nLC Virtual Instrument for Xcalibur Quick Reference Version A
Contents
1. SecureBlackbox YCL edition Size 95 10MB 2 In the list of installed programs 3 4 m Sony Ericsson Bluetooth Remote Control 4 00 Size 4 55MB locate Thermo EASY nLC adden E Seunemn ae i g SQL Server System CLR Types Size 0 81MB Xcalibur VI Select 1t and click m i Thermo EASY nLC Xcalibur I 1 1 Size Click here for support information Used Remove Add Remove Windows To change this program or remove it from your computer click Change or Remove Components a Prog ee 9 Change Topmost Clock amp WW Tortoisecys 1 8 31 Set Program Access and Defaults Total Commander Remove or Repair Y Totaledit jB UC 232A USB to Serial j UltraEdit 32 Uninstall Remove button Co nfiguration To configure the EASY nLC VI software for the Xcalibur data system 1 Start the Instrument Configuration Instrument Configuration program for configurating Xcalibur aea e devices All V Enable multi user login Available Devices Configured Devices Note You can access Help at any E aiii time by pressing F1 All available devices are listed in the Available Devices box all configured devices are listed in the Configured Devices box 2 Make sure that Device Types is set to All or AS AutoSampler Thermo EASY nLC VI now appears in the Available Devices box The EASY nLC VI for Xcalibur device does not appear if the device type is set to LC lt lt Remove Configure Done Help2. keyboard Additional Visit www thermofisher com to find your local Thermo Fisher Scientific representative Support Trademarks EASY nLC is a trademark and Xcalibur is a registered trademark of Thermo Fisher Scientific Inc in the United States
3. If a connection is not established the status bar changes to red If an antivirus program or firewall is blocking 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 Default parameter values for the EASY nLC autosampler and solvent names are configured in the lower portion of the configuration dialog box In the Autosampler Configuration area you can configure the EASY nLC system to use Autosampler ASA or Autosampler ASC You can also configure the selected autosampler for 96 or 384 well plates and a 4x6 ASA or 6x8 ASC vial layout Note All plate formats for the Autosampler ASC have six extra vial positions 1 V1 to 1 V6 on the side 7 Configure additional parameters by Thermo EASY nLC Configuration clicking Edit E4aSY nbC Network Configuration 172 22 50 100 The IP Address can be Found in the The Thermo EASY nLC Sample ee E 172 22 50 100 About box on the EASY nLC instrument wee T dmi Run samples as this user User must Position Selector dialog box opens ser name admin a hes LE device driver and instrument information LC device driver LOServer 1 1 0 1 Le Instrument Proxeon Biosystems 4 5 E45 nbc HPLC Driver Info 2 7 640 Serial Number bC 000100 Loop volume 20 pl Column setup Tao column Idle flow rate 0 0 nlimin IFZ Enabled Idle mixture 5 5 Autosampl
4. 1 with the correct value If you choose to specify the injection volume manually in the Inj Vol column ensure that the injection volume is sensible and complies with the other parameters in the method file for example load volume IMPORTANT The Xcalibur 2 1 data system does not accept the 1 value in the Inj Vol column that is methods will not start This means that you must enter the injection volume in the Inj Vol column which will always overrule the value set in the EASY nLC method file Running a Torun a single sample in the Xcalibur data system Sample 1 Mark the specific row in the sequence Win Genuence S 2 q u 2 n C 2 table Acquisition Options User admiri nstrument Start Instrument 2 Choose Actions gt Run This Sample Thermo EASY nLC VI Yes r Run Rows 1 or click the Run Sample icon in the i toolbar f Priority Sequence M Start When Ready Change Instruments Processing Actions Instrument Method To run a sequence in the Xcalibur data a e M Quan system Shut Down Browse Eo Choose Actions gt Run Sequence or Programs Pre Acquisition Browse Post Acquisition Browse Run Synchronously V Pre Acquisition V Post Acquisition Programs click the Run Sequence icon in the toolbar Prior to execution of the sample or After Sequence Set System sequence run the Run Sequence zi a e On C Standby Off dialog box opens For guidance on how to set up this dialog box refer to C
5. 3 Select Thermo EASY nLC VI in the Available Devices box and click Add to move it to the Configured Devices box 4 Select Thermo EASY nLC VI in the Configured Devices box and click Configure The Thermo EASY nLC Configuration dialog box appears 5 Type the IP address of the EASY nLC Thermo EASY nLC Configuration system and your user name in the EASY nLC Network Configuration a The IP Address can be Found in the ap P r op rate boxes IP Address Hostname About box on the B amp S nbC instrument User name dmi Run samples as this user User must You must have an account on the admin A allstars EASY nLC system with the same user Click Test Connection to test the connection name LE device driver and instrument information LC device driver LOServer 1 1 0 1 The default user name is admin but you can change this to any existing user account on the EASY nLC system eee Autosampler Configuration Solvents For LO Pump Note The EASY nLC IP address tea 6h lt a tt i S OC r Moa me is listed in the About box which Plate installed a GC eeto you can open by pressing the Sample layout Row First Start pos Al ACEROnICrIe THERMO logo in the upper left corner of the touch screen Ok ei 6 Click Test Connection to test the connection to the EASY nLC system If the connection is established the status box to the right of the Test Connection button changes to green see the next figure
6. connection between the EASY nLC instrument and the computer running the Xcalibur application To set up this connection contact local IT support and consult the EASY nLC user manual IMPORTANT Avoid IP conflicts with other units on the network especially the mass spectrometer Refer to your mass spectrometer vendor for assistance in setting up the network connection between the host computer and additional peripheral units to the mass spectrometer e Access through port 6666 for connection to the EASY nLC instrument e Connecting the EASY nLC instrument and the mass spectrometer with the contact closure cable and configuring the EASY nLC system for one way contact closure For further assistance refer to the EASY nLC or mass spectrometer manual as appropriate Revision A 60053 97001 i h 2010 Thermo Fisher Scientific Inc ermo All rights reserved SCIENTIFIC Thermo Fisher Scientific is not responsible for problems that occur as a result of failure to comply with these instructions Installation To install the EASY nLC Virtual Instrument software 1 Close all running programs before i Thermo EASY nLC Xcalibur VI 1 1 InstallShield Wizard starting the installation Remember Welcome to the InstallShield Wizard for to remove earlier versions of the Thermo EASY nLC Xcalibur VI 1 1 EASY nLC VI for the Xcalibur Thermo s SCIENTIFIC The InstallShield R Wizard will install Thermo EASY nLC Xcalibur application befor e insta
7. ASY nLC Xcalibur VI 1 1 to C Program Files Thermo Instruments LC Devices Thermo Change F EASY nLC Xcalibur I e Click Change to specify a different aar aai folder location and then click Next Thermo Fisher Scientific recommends that you install the EASY nLC VI software for the Xcalibur data system in the default destination folder Change button 7 Continue to follow the instructions i Thermo EASY nLC Xcalibur VI 1 1 InstallShield Wizard in the InstallShield Wizard through the rest of the installation until you InstallShield Wizard Completed Thermo SCIENTIFIC The InstallShield Wizard has successfully installed Thermo EASY 8 On the Ins tall S hiel d Wizar d nLE Xcalibur VI 1 1 Click Finish to exit the wizard Completed page select the Log Off Windows Now check box if it is not already selected Thermo EASY nLC for Xcalibur VI requires you to log off and log back on to complete the installation 9 Click Finish to close the wizard and automatically log off reach the final page Log off reboot is required to complete installation Log off Windows now The installation is complete when Log off required you log back on ree Removi nga To remove a previously installed version Previ 0 us 1 Start Add or Remove Programs by E Add or Remove Programs Version choosing Start gt Settings gt Control cessive aade gt P anel SS Remote Control USB Driver Size 3 62MB
8. EASY nLC Virtual Instrument for Xcalibur Quick Reference This guide describes how to install configure and use the Thermo EASY nLC Virtual Instrument VI software with the Thermo Xcalibur 1 1 0 3 data system You must be familiar with the Xcalibur application to proceed For further guidance on Xcalibur specific operations refer to the Xcalibur user manual Contents e Prerequisites e Installation e Removing a Previous Version e Configuration e Creating Methods in Xcalibur e Creating Sequence Runs in Xcalibur Running a Sample Sequence e Monitoring the Status e Sample Information e Additional Support e Trademarks Note When creating EASY nLC methods and executing sample sequence runs you must use the EASY nLC Virtual Instrument VI application with the Xcalibur data system For all other operations such as configuration and maintenance tasks use the touch monitor on the EASY nLC instrument itself Prerequisites Before installing the EASY nLC Virtual Instrument software ensure the following e Installation of Xcalibur version 1 4 or 2 0 prior to installation of the EASY nLC VI software e Administrator rights to install the EASY nLC VI software for the Xcalibur application e Removal of any earlier version of the EASY nLC VI from the target computer prior to installing the new version For guidance on how to remove the EASY nLC VI software see Removing a Previous Version on page 3 e A network
9. ancel Help the Xcalibur user manual or press F1 to access the Help Monitoring To monitor EASY nLC status in the Xcalibur data system the Status e After installing and configuring the a EASY nLC VI software and re e connecting the instrument to the Ese smn Xcalibur data system check the status an in the Status pane of the Xcalibur EERSTE Roadmap Home Page A status pr Lote message also appears Di M Setu e To check EASY nLC method progress i information and other EASY nLC Pump A Desired flow l min Position pl Rigi a eview hardware readouts in real time click eco Sq Real flow n min Ready To Download at the top of Sir the Status pane eee osition Valve B Pasition Valve S Position For Help press F1 5 5 2010 11 03 Sample Using the Qual Browser application you can access sample information and EASY nLC method Information information in the raw MS data Use any of these methods y e On the Xcalibur Roadmap Home Page click the Qual Browser icon e Open the MS raw file that you want to access method information from e Choose View gt Report gt Sample Information to view sample information e Choose View gt Report gt Instrument Method to view method information from all devices used to acquire the data typically the EASY nLC instrument and a mass spectrometer e Navigate through the pages using the arrow buttons in the toolbar or the arrow keys on the
10. calibur user manual or press F1 to access the Help In the Samples area click Select Vials to change the default well or vial selection The Thermo EASY nLC Sample Position Selector dialog box appears Select the specific wells or vials that you want to run in any order The wells or vials will run in the order that you marked them Specify a starting position by clicking the plate Type the number of additional samples to select in the Number of Samples to Select box and click Select The consecutive wells and vials are then selected according to the option set in the Sample Selection Layout area You can change the layout by selecting the Row First or Column First option New Sequence Template General Base File Name PO Starting Number lz Path FO Browse Instrument Method iC Browse Processing Method Browse Calibration File E Samples Number of Samples Mo Tray Type Injections per Sample ho Initial Vial Position al V Re Use Vial Positions Base Sample ID Select Vials Bracket Type C None f Open C Non Overlapped C Overlapped Calibration Qc Add Standards M Add OCs E m C m Cancel Save As Default Help Thermo EASY nLC Sample Position Selector Plate rack Sample selection layout Sample positions click on plate or Select button Row first Initial position Number of samples to select 53 r 7 Column first rrr Select Cance
11. er Configuration Solvents For LE Pump Autosampler Autosampler AST A water Plate installed 6x8 vials r Edit B acetonitrile Sample layout Row first Stark pos Al Cancel Edit button 8 Select the default sample position Thermo EASY nLC Sample Position Selector first sample to be run by clicking a Plate rack position in the Plate Rack area You can subsequently define a new default start position by clicking Clear All and then selecting a new position You can define the sample selection layout by selecting the Row First or Column First option in the lower left Sample selection layout Sample positions click on plate por tion of the dialog box Row first Initial position 1v1 Number of samples to select o 9 Click OK to save your changes and AES exit the Thermo EASY nLC Sample Position Selector dialog box _ 10 Click OK to exit the Thermo EASY nLC Configuration dialog box Creating To create EASY nLC methods in the Xcalibur data system Methods in 1 Choose GoTo gt Instrument Setup or click the large Instrument Setup icon on the Xcalibur Xcalibur Roadmap Home Page All installed devices are represented by icons in the left pane of the Instrument Setup window The icon of your mass spectrometer will appear here Notes e Method information from all installed devices LC MS and so on are saved all together in one method file Remember to define all parameters for al
12. l 6 Click OK to return to the New Sequence Template dialog box Note The position codes for the six extra vials on the side Autosampler ASC are 1 V1 to 1 V6 7 Click OK to create the sample sequence All the sequence information is then listed in the Sequence Setup view on the Home Page Sample Type File Name Sample ID Path Inst Meth Position Inj Vol Unknown 01 Al C CALIBURAD ATA C caliburvmethods Morten Al Unknown Oe Ae CS CALIBURAADAT AS C caliburimethods Morten Ae Unknown 03 AS C CALIBURAAD ATA C caliburvmethods Morten AS Unknown 04 Ad CASCALIBURSDATA C Wicaliburvmethods Morten Ad Unknown 05 AB CAS CALIBURADAT AS C caliburvmethods Morten AA Note The sequence table contains a column called Inj Vol injection volume If the column does not appear choose Change gt Column Arrangement and add the Inj Vol column to the displayed columns The value specified in this column overrules the value specified in the EASY nLC method as long as the value is between 0 and 48 pL This allows you to edit the injection volume of specific samples without changing the EASY nLC method To ensure that the injection volume specified in the method file is used as intended the default value in the Inj Vol column is set to 1 an invalid injection volume When the Xcalibur application detects the invalid value during a run it automatically takes the actual injection volume from the corresponding method file overwriting the
13. l devices when creating new methods e The injection volume sample pickup volume is set in the method file as it has to be coordinated with the rest of the method parameters primarily the loading volume You can override the injection volume in the Xcalibur sequence table however Thermo Fisher Scientific generally discourages doing so having carefully considered all the method parameters Creating Sequence Runs in Xcalibur pA Click the Thermo EASY nLC icon and create your method The Xcalibur method editor is essentially similar to the method editor installed in the EASY nLC software For instructions on how to set up methods refer to the EASY nLC user manual Save the method before exiting the Instrument Setup window me Untitled Instrument Setup File Thermo EASY nLC VI Help osa S x Sample pickup and loading Sample pickup Thermo Volume O pl Max is loop size 2 pl EASY nLC YI Flow O pl min Sample loading SHC Volume 0 pl a ea Flow ul Z min Max pressure Bar Solvents A water B acetonitrile To create sample sequence runs in the Xcalibur data system Choose View gt Sequence Setup View or click the large Sequence Setup icon on the Roadmap Home Page Choose File gt New or click the New icon in the toolbar to create a new sequence template For guidance on how to set up parameters in the New Sequence Template dialog box refer to the X
14. lling the new I 1 1 on your computer To continue click Next version of the software 2 Locate the new version from the Start menu choose Start gt Run and i WARNING This program is protected by copyright law and browse to the location of the international treaties EASY nLC VI Installer exe file 3 Select EASY nLC VI Installer exe and click Open 4 When the Welcome page of the Thermo EASY nLC Xcalibur VI 1 1 InstallShield Wizard opens click Next 5 Carefully read the License Agreement i Thermo EASY nLC Xcalibur VI 1 1 InstallShield Wizard before accepting it Click Next License Agreement Please read the following license agreement carefully THERMO EASY nLC VI SOFTWARE LICENSE AGREEMENT Rev N BY CLICKING THE ACCEPT BUTTON OR OPENING THE PACKAGE YOU ARE CONSENTING TO BE BOUND BY AND ARE BECOMING A PARTY TO THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT CLICK THE DO NOT ACCEPT BUTTON IN THE EVENT YOU DO NOT ACCEPT ALL THE TERMS OF THIS AGREEMENT YOU MAY REJECT THE AGREEMENT AND RETURN THE SOFTWARE TO THERMO FISHER SCIENTIFIC FOR A FULL REFUND WITHIN TEN v QI do not accept the terms in the license agreement 6 On the Destination Folder page do i Thermo EASY nLC Xcalibur VI 1 1 InstallShield Wizard one of the following Destination Folder e Click Next Click Next to install to this folder or click Change to install to a different Folder or Install Thermo E
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