Quick Start Guide - Chromeleon 7.2
Contents
1. Page 22 Quick Start Guide Chromeleon 7 e Select the smallest peak in the chromatogram that you want to be detected the minimum area will be set to 90 of the area of the selected peak Click Next 8 Use the drop down Channel menu to select the channel and the Injection Type field to specify which data the integration settings will apply to Click Finish 9 Click the Chromeleon icon and select Save gt Save from the menu to save the updated processing method The Cobra Peak Detection Wizard determines the best initial integration settings for a chromatogram For simple chromatograms where all peaks are well resolved these settings will be ideal For complex chromatograms or where peaks are only partially resolved the addition of further detection parameters may be required 2 6 3 2 Modifying an existing Processing Method 2 6 3 2 1 Insert a New Detection Parameter To insert a new detection parameter follow these steps 1 Click in the chromatogram plot 2 Click the Processing tab 3 Ifnot already shown display the detection parameters in the chromatogram by clicking Detection Parameters in the Detection Parameters group 4 Click the arrow on the Insert S button Quick Start Guide Page 23 Chromeleon 7 5 Select the appropriate detection parameter from the list The most frequently needed parameters are listed here If you need other detection parameters select Other Parameter2. 7 9 If necessary change the injection names injection types injection positions and other entries For an overview of injection types refer to section 3 3 1 2 The sequence is now visible in the Chromeleon Console s Navigation Pane Quick Start Guide Page 13 Chromeleon 7 2 5 Acquiring Data 2 5 1 Starting an Analysis After the sequence has been created and the instrument is ready you can start data acquisition 2 5 1 1 Checking that the Instrument is Ready 1 In the Console choose the Instruments category Select the instrument by clicking its name in the Navigation Pane In the Work Area select the ePanel tab for the required module To check the baseline for example select the detector s ePanel and click the Monitor Baseline button When you are satisfied that the instrument is ready for analysis start the sequence 2 5 1 2 Starting the Sequence 1 Zz Select the Data category in the Console In the Navigation Pane select the sequence you want to run by clicking on it The Sequence then opens in the Work Area Do one of the following e Click the down arrow on the Start button Click Add to Queue OR e Clickthe S __ button on the Sequence Control Bar above the injection list to add the sequence to the queue and immediately start the queue Page 14 Quick Start Guide Chromeleon 7 The sequence is added to the queue If the queue is empty a Ready Check is performed an
3. For a list and further details on all Chromeleon detection parameters see Detection Parameters Overview in the Chromeleon Help 6 Move the cursor to the location in the chromatogram where you want to insert this parameter and click The new detection parameter is placed in the chromatogram and peak integration is automatically updated Detection parameters have a tag which shows details of the parameter and a vertical dashed line which shows the exact point of the detection parameter in the chromatogram 2 6 3 2 2 Move Modify and Delete Detection Parameters 1 Click in the chromatogram plot 2 Click the Processing tab 3 If not already shown display the detection parameters in the chromatogram by clicking Detection Parameters in the Detection Parameters group 4 Inthe Pointer Zoom group ensure that the Automatic h tool is selected To Move a Detection Parameter e Drag the detection parameter to the required location you can drag a detection parameter by its tag or line Page 24 Quick Start Guide Chromeleon 7 To Edit the Value of a Detection Parameter e Double click the tag and select a new setting from the list To Change the Type of Detection Parameter e Right click on the detection parameter and select Edit Detection Parameter The Edit Cobra Detection Parameter dialog box opens e Select a new detection parameter type from the Parameter Name field and set any parameter values needed e C
4. Quick Start Guide Chromeleon 7 e Instrument Audit Trails A log of instrument events such as system settings executed commands and error messages A sequence is a collection of injections that are analyzed and processed together in series Each injection is represented by a row in the sequence replicate injections are represented with multiple rows Injections can have one of the following Injection Types co e 2 Unknown A sample for which the quantity presence or absence of components is to be determined during the analysis E Calibration Standard A sample with known concentration s of component s Calibration Standards are used in the construction of calibration curves Check Standard A sample with known component concentration s Check Standards are used to verify a calibration e n Blank An injection used to characterize the background signal baseline and or to ensure that unwanted components are not detected Blank injections can be made without an actual injection taking place cro Matrix The sample matrix The peak areas in the Matrix can be subtracted from the corresponding peak areas in all the other injections in the sequence e Unspiked An Unknown sample to be analyzed with the Standard Addition method Quick Start Guide Page 55 Chromeleon 7 o Spiked An Unknown sample to be analyzed with the Standard Addition method with known amounts of components added 3 3 1 3 eWo
5. follow these steps 1 Inthe Console choose the Instruments category and click your instrument s name in the Navigation Pane 2 Select the ePanel tab for the required module in the Work Area for example Pump Page 6 Quick Start Guide Chromeleon 7 3 On the ePanel click Connect Note The ePanel sets are generated automatically to support modules from a specific instrument series e g UltiMate 3000 ICS 5000 When combining modules from these instruments ePanels for some modules may not be displayed automatically See Managing ePanel Sets and ePanels in the Chromeleon Help for details on manually adding ePanels to a set 2 3 3 Controlling and Monitoring the Instrument Usually samples are analyzed as part of a sequence using a predefined set of instrument commands stored in an Instrument Method Sometimes typically between sequence runs it is necessary to issue individual commands to the instrument modules such as for starting or stopping the flow setting eluent composition switching on or off the detector lamp or monitoring the baseline To issue instrument commands follow these steps 1 In the Console choose the Instruments category Select the instrument by clicking its name in the Navigation Pane 2 Inthe Work Area select the ePanel tab for the required module 3 Use the controls on the ePanel to issue instrument commands for example setting the wavelength of a UV VIS detector or starting mobile ph
6. selecting TIC skip steps 4 and 5 4 Optional If SRM data was acquired type in the mass in the Precursor Mass field If a large number of acquisition filters exists this will assist you in limiting the selectable filters to only those of interest Figure 15 Precursor Mass XIC Mass es or Ranges gt 174 c ESI SRM ms2 163 05 cid0 00 58 10 58 10 73 00 73 00 106 00 106 00 c ESI SRM ms2 190 00 cid0 00 109 00 109 00 145 00 145 00 173 00 173 00 c ESI SRM ms2 192 10 cid0 00 105 00 105 00 132 00 132 00 160 00 160 00 c ESI SRM ms2 202 00 cid0 00 68 00 68 00 124 00 124 00 132 00 132 00 c ESI SRM ms2 202 00 cid0 00 92 00 92 00 131 10 131 10 175 00 175 00 c ESI SRM ms2 208 10 cid0 00 70 10 70 10 89 10 89 10 116 10 116 10 iseti c ESI SRM ms2 210 10 cid0 00 65 10 65 10 93 00 93 00 111 10 111 10 c ESI SRM ms2 216 10 cid0 00 96 10 96 10 104 00 104 00 174 10 174 10 XIC Mass es or Range s Figure 15 Filtration of scan list by entering SRM precursor mass 5 Type in a SIM SRM product ion mass or mass range in the XIC Mass es or Range s field Similar to the Precursor Mass field this field will assist in limiting the selectable filters to Page 44 Quick Start Guide Chromeleon 7 only those of interest In addition this field will also define which mass es are used to create the XIC 6 Select the appropriate filter from the Filter field dropdown Based on the combination of
7. template You can navigate through the sequence by e Using the Previous and Next buttons in the Navigation group of the Home tab Page 34 Quick Start Guide Chromeleon 7 e Selecting the injection and or channel you want to view in the Navigation Pane 2 7 2 Printing Results When printing results you can e Print the currently selected injection only e Print the entire sequence Both processes will be described in the following sections Tip With the autorepeat area function you can create a single report template that will be suitable for a range of methods whether a method uses one data channel or several or analyzes only one compound or several Chromeleon will automatically report the relevant results For details refer to Define Autorepeat Areas in the Chromeleon Help 2 7 2 1 Printing Results for a Single Injection To print the results for the currently selected injection 1 Select the Report Designer category from the Chromatography Studio 2 Inthe Navigation Pane select the injection you want to print out 3 On the Studio Menu select Print to open the Print dialog box 4 From the Print dialog box select e Apply to Current Injection e The Printer you want to use Quick Start Guide Page 35 Chromeleon 7 e The Sheets to be printed for the current injection The results for the current injection are now printed 2 7 2 2 Print Results for the Entire Sequence To print results for the enti
8. the Filter and XIC Mass es or Range s an XIC for evaluation will be created in this UI Figure 16 PESTICI Signal pac Type 75 000 Mass Range x Precursor Mass XIC Mass es or Range s 50 000 237 10 90 10 Filter 25 000 c ESI SRM ms2 237 10 cid0 00 72 10 72 10 90 10 90 10 y Smoothing Points ol Wl _ _ ___ __ _ E_ SE ASS RRE ES RS ERRE RSE 10 000 1 725 2 000 2 475 Figure 16 XIC displayed based on parameters Optional steps to set up Confirming XIC for component 7 Click Th to create a new Confirming XIC 8 Repeat steps 3 through 6 to setup the XIC for a confirming peak 9 Click on Enable underneath the Ratio header 10 Set the expected Target Ratio peak area relative to the Quantitation peak 11 Select Relative or Absolute tolerance for the Target Ratio Window Type 12 Set the tolerance Window If the target ratio is set to 50 the Window to 10 the peak area ratios falling within the following windows will result in a confirmed component Absolute 40 60 Quick Start Guide Page 45 Chromeleon 7 Relative 45 55 13 Set the absolute tolerance in minutes for the confirming peak in the lon Coelution field After completion of these steps combined with the steps outlined in section 2 6 it will be possible to review and report out on the resultant data See the Extracted lon Chromatograms section of the Chromeleon Help for m
9. the first time all parameters come populated with recommended default values 2 8 4 3 Component Table Advanced Tab In order to process and quantitate components using XICs from MS data you are required to define a special channel for the desired components In the Channel column of the component table all components being quantitated using an XIC must be set to MS Quantitation via the dropdown Figure 12 and Figure 13 Quick Start Guide Page 41 Chromeleon 7 Detection Component Table Component Table Advanced Calibration Unidentified Peak be Component Table Group Area Drag a column header here to group by that column Run Cor Name RetTime Window Channel Sta Desloratadine d4 1 410 0 500 AG TIC STD Interr Hydroxydesloratadine 1410 0 500 AN MS Quantitation Internal De Desloratadine 7420 OS00AN MSQuantitation werd De Ee ae SEAS TTS ESL AAA SLATES Sg ae ee Ee TIC Seege Figure 12 MS Quantitation selection in Component Table 20130123 Quan A 11 25000000 MS_Quantitation Desloratadine Figure 13 MS Quantitation channel 2 8 4 4 Component Table Properties Extracted lon Chromatograms 1 Select a component by highlighting en entire row in the component table click Show Properties to display the Properties dialog box then select Extracted lon Chromatograms in the properties navigation pane Figure 14 2 Click to create a new Quan
10. which they will be processed and includes injection variables name type etc that characterize each injection Sequences can be created in the Console or by using an eWorkflow eWorkflows are simple but powerful tools for creating sequences based on pre defined templates and rules For more information on creating and using eWorkflows see Creating eWorkflows in the Chromeleon Help You create a sequence using the Sequence Wizard within the Console But first the following files should be prepared e Instrument Method e Processing Method e Report Template 2 4 1 Creating an Instrument Method 1 Inthe Instruments category of the Console select the instrument from the Navigation Pane for which you want to create the intsrument method 2 On the Create menu click Instrument Method 3 Complete all wizard steps and click Finish The created instrument method opens in the Chromatography Studio 4 Review the instrument method by selecting the module views in the Navigation Pane Edit settings if required Quick Start Guide Page 9 Chromeleon 7 5 Save the instrument method using the Save icon dal in the Quick Access Toolbar and specify a location and object name 6 Close the Chromatography Studio 2 4 2 Creating a Processing Method 1 Inthe Console on the Create menu click Processing Method 2 Select one of the predefined layouts and click Next 3 Entera name select a file location and optionally enter a comm
11. 21 Discovery Service 48 Electronic Report 54 61 eWorkflows 50 56 Extracted lon Chromatogram 39 Genesis 41 ICIS 41 Identifying Peaks 26 Injection List 59 Injection Types 55 Instrument 5 53 Instrument Configuration Manager 47 Instrument Controller Service 47 49 Instrument Method 9 54 60 Integration 20 Interactive Results 18 lon Coelution 46 License Manager 47 Mass Range 44 Mass Spectrometry 37 Quick Start Guide Chromeleon 7 Matrix 55 Module 6 Monitor 7 16 MS Channel 39 42 MS Data Visualization 37 MS Instrument Control 37 MS Instrument Method 37 MS Plot 38 Navigation Pane 13 52 59 Overlays 39 Peak Detection 20 41 Plot Mode 38 Precursor Mass 44 Print 35 36 Processing Method 10 29 40 54 Quantitation 30 42 Query 54 Queue 14 Rack View 11 Report 10 34 35 54 61 Report Designer 58 Retention Time 30 Reviewing Data 17 34 Ribbon 59 Scheduler 47 Sequence 9 10 36 54 Services Manager 47 SmartPeaks 25 Spectral Library 54 62 Spiked 56 Start 4 Studio 17 50 57 Studio Menu 59 62 Target Ratio 46 TIC 44 Unknown Injection 55 Unresolved Peaks 25 Unspiked 55 User Manager 48 Work Area 52 59 XIC 39 45 46 Page 63 www thermoscientific com Australia 61 3 9757 4486 Austria 43 1 333 50 340 Belgium 32 53 73 42 41 Brazil 55 11 3731 5140 China 852 2428 3282 Denmark 45 70 23 62 60 France 33 1 60 92 48 00 Germany 49 6126 991 0 India 91 22 2764 2735 Italy 39 02 51 62 1267 Japan 81 6 6885 121
12. 3 Korea 82 2 3420 8600 Netherlands 31 76 579 55 55 Singapore 65 6289 1190 Sweden 46 8 473 3380 Switzerland 41 62 205 9966 Taiwan 886 2 8751 6655 UK Ireland 44 1442 233555 USA and Canada 847 295 7500 Thermo SCIENTIFIC Part of Thermo Fisher Scientific
13. Every analysis using Chromeleon follows the same 6 basic steps Start Chromeleon Start the instrument Create a sequence 1 2 3 4 Acquire data 5 Process data 6 Review and report results This Quick Start Guide provides enough information to perform each of these 6 steps as part of a simple analysis For more advanced use of Chromeleon including performing more complex analyses please refer to the Chromeleon Help Note It is assumed that Chromeleon has been installed and at least one instrument has been connected and configured For details on installation and connecting and configuring instruments see the Installation Guide Quick Start Guide Page 3 Chromeleon 7 2 2 Starting Chromeleon To start the Chromeleon software e Double click the Chromeleon 7 icon on the desktop ze human H OR e Use the Windows Start menu Select Start gt All Programs gt Chromeleon 7 gt Chromeleon 7 The Chromeleon Console window opens If user management is active you will be prompted to log on to the software Enter the credentials provided by your Chromeleon adminstrator to proceed Page 4 Quick Start Guide Chromeleon 7 2 3 Getting your Instrument Started To control and monitor an instrument in Chromeleon you must e Make sure the Instrument Controller Service is running e Establish a connection 2 3 1 Making sure the Instrument Controller Service is Running The Chromeleon Instrument Controller Ser
14. Introduction 1 1 About this Document This Quick Start Guide provides a quick reference to help get you started with Thermo Scientific Dionex Chromeleon It is recommended that you review the Quick Start Guide thoroughly before working with Chromeleon The Quick Start Guide has two parts Using Chromeleon Guidance in starting a simple analysis processing the data and reporting the results Appendix Chromeleon An overview of the Chromeleon Overview interfaces and common features This Quick Start Guide is provided as is Every effort has been made to supply complete and accurate information and all technical specifications and programs have been developed with the utmost care However Thermo Fisher Scientific assumes no responsibility and cannot be held liable for any errors omissions damage or loss that might result from any use of this manual or the information contained in it Quick Start Guide Page 1 Chromeleon 7 1 2 Other Documentation Chromeleon is provided with other documents that will help you to learn more about the software Their scope is described in the Document Overview which is delivered in printed form with the Chromeleon installation media but also available in electronic form on the installation disk in the Documents folder The Chromeleon Online Help is available in electronic form in the Online Help folder Page 2 Quick Start Guide Chromeleon 7 2 Using Chromeleon 2 1 Overview
15. RA3 100 000 Chrom_InstMet Chrom_ProcMet Interrupt 05 07 2013 18 55 48 WI 10 None Injection 10 Unknown RA4 i 100 000 Chrom_InstMet Chrom_ProcMet Idle 11 None 3 Injection 11 Unknown RA4 i 100 000 Chrom_InstMet Chrom_ProcMet i Idle 12 None E Injection 12 Unknown RA4 100 000 Chrom InstMet Chrom_ProcMet Ide D y i es f f SCT Name a Type Date Modified Comment 74 Chrom_InstMet Instrument Method 14 06 2013 15 02 M Chrom_ProcMet Processing Method 14 06 2013 15 06 i N Associated items Custom Sequence Variables 0 cmadmin Full Access Figure 18 Chromeleon Console Category Bars Status Bar Quick Start Guide Page 51 Chromeleon 7 1 2 3 Category Bars Use the category bars to switch between the three categories Instruments Data and eWorkflows Figure 19 A Instruments CH eW orkflows Figure 19 Category Bars Navigation Pane Here you can navigate the objects related to the selected category Work Area This area shows the content of objects selected in the Navigation Pane Here you can work on Chromeleon objects There are three additional parts for user interaction The Navigation Pane has a top level filter that lets you control which instruments data vaults or eWorkflows are displayed a b C d Ze Local Items available on the local Chromeleon station All Items avai
16. Results Hise nee cere ee eee 34 2 7 2 Printing TEE 35 Quick Start Guide Page i Chromeleon 7 28 MSI Chro melon aio ise latas 37 2 8 1 MS Instrument Control 37 2 8 2 Acquiring Data with an MS OL 2 8 3 MS Data Visualization aannaaannnnnnnnnnnnnnnnnrnnnnnrnnn 37 2 8 4 MS Data Processing Processing Method 40 3 Appendix Chromeleon OvervieW sses 47 SG MED Lee ele teg O O 47 3 2 Instrument Controller Service 49 3 3 gt ChHrOMEIEON Eet SEA AE EE ee 50 3 3 1 ChromeleonConsole 51 3 3 2 Chromatography Studio 57 Page ii Quick Start Guide Chromeleon 7 Copyright Copyright 2013 Thermo Fisher Scientific The information contained in this document is subject to change without notice All rights reserved including those for photomechanical reproduction and storage on electronic media No part of this publication may be copied or distributed transmitted transcribed stored in a retrieval system or transmitted into any human or computer language in any form or by any means electronic mechanical magnetic manual or otherwise or disclosed to third parties without the express written permission of Thermo Fisher Scientific Inc Trademarks Windows Windows Vista SQL Server 2008 SQL Server and Microsoft are registered trademarks of Microsoft Corporation All other trademarks are property of Thermo Fisher Scientific Inc and its subsidiaries Quick Start Guide Page iii Chromeleon 7 1
17. Working with Chromatograms e Detecting and Integrating Peaks e Identifying Peaks e Calibration and Quantitation 2 6 2 Working with Chromatograms You can view the integrated chromatogram of the current injection in the chromatogram plot Figure 5 If the evaluation of data is not what you want you can for example change the peak delimiters and the baseline directly in the chromatogram Of course you can adapt the layout of the chromatogram to your needs It is also possible to overlay other chromatograms for comparison For details refer to Working with Chromatograms in the Chromeleon Help Quick Start Guide Page 19 Chromeleon 7 3 Injection 1 Alkylphenones 1 UV_VIS_1 1 Acetanilide 2 Acetophenone 3 Propiophenone 2 Acetophenone 0 246 mAU Smoothing 0 020 BLNoiseEnd dPeak d On 3 Propiophenone 0 363 joiseStart MinArea 0 1000 4 i 4 TailSensFac 1 000 AAA Figure 5 Chromatogram Plot Tip You can overlay chromatograms from different injections or channels by using the pins F in the Navigation Pane or by selecting the channels in the Navigation Pane to select two or more channels hold down CTRL or SHIFT and then click the channels 2 6 3 Detecting and Integrating Peaks For correct quantification or qualification of a chromatogra
18. andard calibration using a single component standard at multiple concentrations Chromeleon supports various methods of calibration including internal standards and standard addition For information on using these methods of calibration see Calibration and Amount Calculation in the Chromeleon Help To perform a simple calibration in Chromeleon you need to e Specifiy which injections are Calibration Standards e Create Calibration Levels and assign these to the Calibration Standards Page 30 Quick Start Guide Chromeleon 7 e Enter the amount or concentration of the Calibration Standards e Review the calibration curve 2 6 5 1 Specifying which Injections are Calibration Standards Calibration standards are marked as such in the injection list 1 Click the Injection List Category in the Chromeleon Chromatography Studio window 2 For each Calibration Standard injection click in the Type field and select Calibration Standard from the list of types 2 6 5 2 Creating and Assigning Calibration Levels 1 Click the Injection List Category in the Chromeleon Chromatography Studio window 2 Click in the Level cell for the first calibration standard and select Create new level The value 01 is added Assign this level to all injections of this calibration standard 3 Repeat Step 2 for all calibration levels 2 6 5 3 Entering Calibration Standard Amounts or Concentrations 1 Click the Data Processing Category in the Chromeleo
19. ase flow on a pump When an analysis is running you can monitor instrument parameters and outputs such as the detector signal output or pump pressure from the module s ePanel To monitor the detector signals without starting a sequence click Monitor Quick Start Guide Page 7 Chromeleon 7 Baseline on the toolbar above the ePanel set Click the same button again to stop monitoring the baseline You can also save the monitor baseline data For details see Monitor the Baseline in the Chromeleon Help Note Most common commands are available from the ePanels If you need to execute a command that is not available you can access all available instrument commands from a dialog box that is accessible via the Command button CL sOi Comman 2 in the Instruments toolbar Tip For certain instruments Chromeleon provides procedures for automatically starting or shutting down a chromatography system or setting it into standby mode These procedures are referred to as Smart Startup Smart Shutdown and Smart Standby respectively For details of which instruments can be controlled in this way and how to use this functionality see Smart Startup Smart Shutdown and Smart Standby in the Chromeleon Help Page 8 Quick Start Guide Chromeleon 7 2 4 Creating a Sequence A sequence determines how a group of injections should be processed The injection list is the primary element of the sequence The list groups injections in the order in
20. ate window that is launched from the Console in which you can work with data and objects related to a selected sequence Here you can view and optimize all aspects of the data modify instrument methods and processing methods define and generate reports and manage spectral libraries Quick Start Guide Chromeleon 7 3 3 1 Chromeleon Console When you start Chromeleon 7 the Console is the first window to appear The Console window has three major parts Figure 18 Navigation Pane Sequence Control Bar Work Area EE eas Back Create File Edit View Tools Help Data Chromeleon NO Fite Y Ru inning stop EJ cGER D inning DR I ChromeleonLocal i 3 Studio Y Print Py Up Insert Row HH Fill Down BO Lock Y Filtering Grouping f Custom Columns amp Find Nat E Instrument Data a Ki StationQualification D Runs E i Sequences 5 3 Injection 5 Unknown RA2 l 100 000 Chrom_InstMet Chrom_ProcMet Finished 18 06 2013 15 23 19 e e G IN MS A p Name Type Position R Volume ull instrument Method Processing Method Status Inject Time Levei E FLD_Data E 025546_Spectra_Se 2 MaA ey uonoaluy Injection 6 Unknown RA2 100 000 Chrom_instMet Chrom_ProcMet Finished 18 06 2013 15 47 46 done E EE 2 A a Injection 7 Unknown RA3 100 000 Chrom_InstMet Chrom_ProcMet Interrupt 18 06 2013 16 11 00 E Irjecion8 Unknown
21. d they can be used for reporting or results calculations When reporting it is useful to name components in a chromatogram When performing Calibration and Quantification it is essential that at least the calibration peaks in a chromatogram are named Page 26 Quick Start Guide Chromeleon 7 The process of assigning a name to a component is called identification The names and expected retention times of named components are stored in a Chromeleon component table The following sections describe how to e Create a component table e Update the expected retention times and windows 2 6 4 1 Creating a Component Table There are three ways to create a component table e Via the Component Table Wizard e Interactively in the chromatogram pane e Via the component table processing method 2 6 4 1 1 Via the Component Table Wizard To create a component table by using the Component Table Wizard 1 Click in the chromatogram plot 2 Click the Processing tab 3 If not already shown display the peak windows in the chromatogram by clicking Peak Windows M in the Component Table group 4 Click the Component Table Wizard button AN The Component Table Wizard dialog box opens The 5 page wizard guides you through the process of naming components On the first 4 pages you can specify whether to Quick Start Guide Page 27 Chromeleon 7 keep existing components adding new components to the existing ones the ti
22. d the queue is started if there are no errors Figure 3 Chromeleon lH Save Studio Print mul Up gt Insert Row H Fill Down a Lock Y Filtering Grouping f Custom Columns Position Volume kl Instrument Method Processing Method RAI 100 000 Chrom_InstMet Chrom_ProcMet Main joey uonoalu a 100 000 Chrom_InstMet i Chrom_ProcMet i 4 None 3 Injection 4 Unknown RA2 i 100 000 Chrom_InstMet Chrom_ProcMet Idle Figure 3 Running Sequence Note The Chromeleon Queue can be used to schedule multiple sequences to run in succession See Managing Queues in the Chromeleon Help for information on using Queues Tip With Chromeleon you can automatically start or shut down a chromatography system or set it into standby mode This is called Smart Startup Smart Shutdown and Smart Standby For details of the supported instruments and how to use this funtionality see Smart Startup Smart Shutdown and Smart Standby in the Chromeleon Help Quick Start Guide Page 15 Chromeleon 7 2 5 2 Monitoring an Ongoing Analysis During analysis it is useful to monitor the detector signal and other instrument parameters such as pressure and temperature To monitor an ongoing analysis 1 Inthe Console choose the Instruments category and click your instrument s name in the Navigation Pane 2 Select the Home ePanel in the Work Area to monitor the detector signal and au
23. dit trail Note The settings of other modules can be monitored on their respective ePanels Page 16 Quick Start Guide Chromeleon 7 2 6 Processing Data After chromatographic or mass spectrometry data has been acquired it can be processed All processing steps are performed in the Studio and saved in a processing method To open the Studio from the Console double click any object in a sequence or click the Studio Studio button Chromeleon has a variety of tools to simplify or speed up data processing tasks such as SmartPeaks but only the most common processing steps are described in this Quick Start Guide Note When you make a change in the processing method the results for all injections in the sequence which use that processing method are recalculated instantaneously There is no need to reprocess the sequence or manually update results 2 6 1 Reviewing Data in the Chromatography Studio After data for all samples in a sequence has been acquired it is useful to review the chromatograms and peak data before reporting the results Often peak detection integration and calibration settings need to be modified before results are reported See chapter 2 6 2 and onwards 1 Inthe Chromeleon Console select the Data category 2 Open the first injection of the sequence in the Chromatography Studio by double clicking an injection in the the Chromeleon Console s Work Area The Chromatography Studio opens Q
24. ent 4 Click Finish to save the processing method and close the wizard The new processing method opens in the Chromatography Studio 2 4 3 Creating a Report Template 1 Inthe Console on the Create menu click Report Template 2 Select one of the predefined templates and click Next 3 Select a file location and enter a file name 4 Click Finish to save the report template and close the wizard 2 4 4 Creating a Sequence To create a sequence using the Sequence Wizard within the Console 1 Inthe Instruments category of the Console select the instrument from the Navigation Pane for which you want to create the intsrument method Page 10 Quick Start Guide Chromeleon 7 2 Inthe Console on the Create menu click Sequence 3 Complete the injection configuration settings for the injections Pattern for Injection Name Number of Vials Injections per Vial Start Position Injection Volume Rack View Figure 2 Specify how injections will be named This is a free text field to which the codes n p i and r can be added Click the button to the right of the Pattern for Injection Name field to see definitions for these codes Specify the total number of vials in the analysis Specify the number of injections per vial in the analysis Specify the sequence start position of the sequence for the analysis This specifies the position of the first vial in the autosampler The wizard automatically
25. icking the component in the calibration table selecting the peak in the ai a Pomannan f chromatogram or by using the 2 Component buttons in the Navigation group of the Data Processing Home tab Quick Start Guide Page 33 Chromeleon 7 2 7 Reviewing and Reporting Results After data has been acquired and calibration performed you can review and report results You can create report templates which output results and other data in any format and layout you require or use one of Chromeleon s default templates This Quick Start Guide gives information on using the default templates only for information on modifying report templates or creating new templates see Designing Reports in the Chromeleon Help To review and report results you must first associate a template with the sequence Once you have done this you can then e Review the results e Print results e Export a report In Chromeleon you can create an electronic report which can include worksheets comprising of chromatograms tables charts calibration curves and other instrument or results values These electronic reports can be subjected to an Electronic Signature process for approval For more information on creating and using electronic reports and the electronic signatures functionality see Electronic Reports in the Chromeleon Help 2 7 1 Reviewing Results The results can be reviewed by clicking the appropriate tab at the bottom of the Work Area of the report
26. ide Page 57 Chromeleon 7 Studio Menu Ribbon Work Area Navigation Pane a A A MN la V Pus Pra Calibrati n Plot TT Peak Properties ka UV Vis Spectra ES injection Rack Results Caib amp PM Contour amp Res 7 keescpur Results 4 Interactive Charts A Fluorescence Spectra JI Mass Spectra Presets Pares Maso 2 Chromeleon 1 ction 1 UV_VIS_4 WVL 300 nm my 50 6 121 o D 26 47 5 827 Am e 49 6 51 6 181 42 6266 46 57 A IN 6700 154 6419 a LEE a ee ae 226 1 Cheromelson 2 Injection 2 UV VIS d e nn 558 570 500 5 90 6 90 5 10 620 6 310 6 40 65 59 6 50 670 SIT Detector Component Table Undentied Fesk Group Tabie Chromatogram Subtraction UV Spectral Library Screening UV Setngs Advanced Setings SST RC 7 Detecton Settings K Algorithm Cobra Run Cobra Wizard Bosetre Noze Range Cobra regen Wan d Ato Range Age bet Sat Tre Consider Void Peak crmadmin Full Access Figure 20 Chromatography Studio Category Bars The Chromatography Studio is structured similarly to the Chromeleon Console and consists of the following major parts e Category Bars Figure 21 These switch the display between the six categories Injection List Instrument Method Data Processing Report Designer Electronic Report and UV Spectral Library Page 58 Quick Start Guide Chromeleon 7 Figure 21 Category Bars e Navigation Pane An area in which you can navigate th
27. il o Os F DOOR d o IGN CH OS O 3 10 CONOS a SO GO O CHIN mg O TOO 3 ic a sg Je O O CIS y OO mee SS O lt lt o ES 4 oO e Osea yj aaa gt gg O OSS aaa he CH E e slk wi LECH e OG q o oo oR Quick Start Guide Chromeleon 7 2 July 2013 7229 0004 Revision 1 0 Chromeleon 7 Table of Contents Ds AAT elt OI EE 1 1 1 About this Document Zeene eet deed ege EA ege 1 1 2 Other Documentation ee EE 2 e Use Cro melenas 3 2i e EE 3 2 2 Starting Chromeleon cooconcocconionocnonnoneononnonnonennonnonnorennennons 4 2 3 Getting your Instrument Started 5 2 3 1 Making sure the Instrument Controller Service is RUDNINE EE 5 2 3 2 Establishing a Connection 6 2 3 3 Controlling and Monitoring the Instrument T 2 4 EIERE 9 2 4 1 Creating an Instrument Method 9 2 4 2 Creating a Processing Method 10 2 4 3 Creating a Report Template 10 2 4 4 Creating a e 10 225 ACQUIFINS Dada riu 14 25 1 Starting an Analisis ic 14 2 5 2 Monitoring an Ongoing Analysis aseseseseeeenennan 16 2 65 PROCESSING Dala EE EE 17 2 6 1 Reviewing Data in the Chromatography Studio 17 2 6 2 Working with Chromatograms oococcocconconcnnonnoninnonos 19 2 6 3 Detecting and Integrating Peaks oscsereneerereennn 20 2 6 4 Identifying Peaks venida 26 2 6 5 Calibration and Ouantitation 30 2 7 Reviewing and Reporting Results 34 2 7 1 Reviewing
28. increments for the following vials Specify the injection volume If your autosampler supports the preview function the rack view provides a graphical representation of the trays and racks that are installed on the selected instrument The preview also allows you to conveniently determine the position of the first sample in the autosampler tray Simply click a vial to specify the required start position The information in the Start Position edit field is automatically updated Quick Start Guide Page 11 Chromeleon 7 na New Sequence Wizard H we Pattem for Injection Name 1 Injection n Number of Vials 5 Seu 1 135 Injections per Vial 3 1 999 Start Position RA1 RA1 B5 Injection Volume 100 000 0 001 100 000 ul Po Y Volume uL Instrument Method E 100 000 2 Figure 2 Rack View 4 Click Next Note When you are creating a sequence using the wizard you can only add injections with type Unknown After the sequence has been created you can modify the injection types and positions 5 Select methods and reporting preferences For each field use the button to navigate to and select the file you want to use When all fields are completed click Next 6 Enter a comment for the sequence optional and click Finish 7 The Save dialog box opens 8 Specify where to save the sequence enter a file name and click Save Page 12 Quick Start Guide Chromeleon
29. k Area lets you edit the instrument method 3 3 2 3 Data Processing When the Data Processing category is selected you can view chromatography and mass spectrometry results edit the processing method and manually integrate chromatograms The Navigation Pane gives an overview of all injections channels processing methods and view settings used in the sequence Chromatographic results are shown in the Work Area You can customize the panes displayed such as Chromatogram Interactive Results Calibration Plot and Processing Method on the Ribbon by selecting or hiding each pane in the Panes group of the Data Processing Home tab Figure 21 Page 60 Quick Start Guide Chromeleon 7 d Deg a ex L Chromategram Processing Method i Contour 30 Piot Wir Plot MS Components 2 ta ML Calibration Pict 7 Peak Properties ka UV Vis Spectra BES injection Rack d EEGEN SemartLink Results Caib amp PM ontour amp Res interactive Resto j Interactive Charts La Flucrescence Spectra IK Mass Spectra Lu Chromatogram Processing Method J Contour 3D Plot We I t Plot MS Components Calibration Plot EN Peak Properties M UV Vis Spectra 35 Injection Rack EE Interactive Results Interactive Charts M Fluorescence Spectra MA Mass Spectra Panes Figure 22 Pane Selection in Ribbon Tip The Presets group left of the Panes group in the Data Processing Home tab offers typical combinations of panes 3 3 2 4 Report Desig
30. lable on the Chromeleon Domain 77 Favorites Filter for displaying commonly used items Y Custom Filter based on text input The Sequence Control Bar above the injection list indicates the sequence status New Running Complete Interrupted Incomplete and can be used to start and stop a sequence It is only available when a Sequence is selected in the Navigation Pane Page 52 Quick Start Guide Chromeleon 7 Note When a sequence is configured to be electronically signed additional statuses are available The Status Bar shows general information such as the currently logged on user 3 3 1 1 Instruments The Instruments category provides access to all instruments on the network this might be limited by user privileges When the Instruments category is selected the configured instruments are displayed in the Navigation Pane The Work Area gives details about the instrument selected in the Navigation Pane From the Work Area you can review instrument status and make changes to instrument parameters Across the top of the work area a series of ePanel tabs are displayed ePanels can be used to monitor instrument operation and to directly control the instrument Note When you select an instrument from the Navigation Pane that is currently offline a message is displayed in the Work Area 3 3 1 2 Data The Data category provides access to all data stored in each connected Data Vault 3 container for all data No
31. lay MS data processing settings click the Processing Method tab of the Data Processing category and select the All Settings layout in the Layouts group Figure 11 Ted e al AA NOTA Basic Quantit Quantitative 3D Quantitative yoo om i S AAA NU E MS Quantitati Qualitative 3D Qualitative All Settings Chromeleon 6 Settings for all processing method options Figure 11 All Settings Selection in Layouts group Page 40 Quick Start Guide Chromeleon 7 2 8 4 1 MS Peak Detection Algorithms In addition to COBRA and Chromeleon 6 algorithms two new algorithms are introduced Genesis and ICIS e Genesis This algorithm is generally used for processing data with noisy baseline such as MS full scan data In some instances the algorithm may also be used with non MS data as well These include but are not limited to UV CD and ED data e ICIS This algorithm is recommended when dealing with data with very low noise or abstracted data such as that acquired in SIM or SRM mode or extracted post acquisition as XICs 2 8 4 2 MS Detection Tab On this tab page in the processing method you can define default MS detection settings or detection settings ona component by component basis In the Extracted lon Chromatogram dropdown all components denoted with are using detection settings specific to that component All other components use default MS detection parameters When selecting the ICIS and Genesis algorithms for
32. lick OK to save the change and close the Edit Cobra Detection Parameter dialog box To Delete a Detection Parameter e Right click on the detection parameter and select Delete Detection Parameters 2 6 3 2 3 Integrate Unresolved Peaks Partially resolved peaks can be difficult to integrate The SmartPeaks integration assistant helps you to integrate these peaks 1 Click in the chromatogram plot 2 Click the Processing tab 3 On the Detection Parameters group click SmartPeaks A 4 Use the cursor to drag a rectangle in the chromatogram around the area that contains the partially resolved peaks The SmartPeaks Select Alternative dialog box opens Figure 6 Quick Start Guide Page 25 Chromeleon 7 SmartPeaks Select Alternative a x Zoom to bas elin F YUNU WI WW get AN 3 Exponentially skimmed riders Advanced ential at both ends rider skin TI Figure 6 SmartPeaks Select Alternative dialog box Tip For more options you can click the Advanced tab in the SmartPeaks Select Alternative dialog box For details of how to use these settings see SmartPeaks Select Alternative in the Chromeleon Help 5 Select the preferred peak detection and click OK 6 The detection parameters in the processing method are now updated and the new detection parameters are shown in the chromatogram 2 6 4 Identifying Peaks After peaks have been detected and satisfactorily integrate
33. m all peaks of interest must be detected and correctly integrated To achieve this you can either e Create a new set of detection parameters OR e Modify an existing processing method For the purposes of this guide it is assumed that the user will first create a new set of detection parameters using the Cobra detection algorithm and then modify these to improve the integration and peak detection Page 20 Quick Start Guide Chromeleon 7 Note On the MS Detection tab page in the Processing Method you can select a peak detection algorithm Chromeleon 6 Cobra Genesis or ICIS for your MS data You can apply the peak detection settings to the entire chromatogram and or you can define different peak detection settings for individual extracted ion chromatograms The defined algorithm and settings apply to this extracted ion chromatogram only For all other data than MS data the detection algorithm can be set on the Detection tab page in the Processing Method 2 6 3 1 Creating a New Set of Cobra Detection Parameters This section gives information on how to set up a new processing method and use the Cobra Peak Detection Wizard to determine the initial integration settings for a chromatogram For more information about creating processing methods see section 2 4 2 1 Open the sequence in the Chromatography Studio by double clicking an injection in the Console and open the Data Processing category Select the chromat
34. me range over which to consider components and a minimum area below which components are ignored On the final page you can name all found components modify the retention time and peak window and add comments Click Finish to save the component table updates and close the Component Table Wizard The chromatogram view in the Chromatography Studio Work Area is automatically updated to display the new component windows 2 6 4 1 2 Interactively in the Chromatogram Pane To add a component from the chromatogram plot 1 2 3 Click in the chromatogram plot Click the Processing tab Activate the Peak Windows option and the Add Component option in the Component Table group Drag a rectangle around the peak you want to add to the component table The peak is added to the component table with a generic name for example Component 1 and the peak window is visible in the chromatogram plot Double click the peak window tag and enter the component name Page 28 Quick Start Guide Chromeleon 7 2 6 4 1 3 Via the Component Table Processing Method To create a component table in the processing method 1 Click the Data Processing Home tab 2 Inthe Panes group click Processing Method to display the processing method Tip You can maximize screen space by hiding the other panes and view the processing method only In the Panes group disable the panes that are not currently needed 3 Inthe processing method select the C
35. n Chromatography Studio window 2 Inthe Panes group of the Data Processing Home tab click Processing Method 3 Inthe processing method select the Component Table tab Figure 7 Quick Start Guide Page 31 Chromeleon 7 4 Detection MS Detection Component Table Calibration Unidentified Peak Group Table Chromatogram Subtractic f Component Table Group Area Drag a column header here to group by that column Run Component Table Wizard Figure 7 Component Table Enter the standard amount for each level of the calibration component in the appropriate cell Level 01 Level 02 etc Calibration curves are updated automatically when you make changes to calibration standards 2 6 5 4 Viewing Calibration Curves You can view the calibration curve s Figure 8 in the Data Processing Category of the Chromatography Studio 1 Click the Data Processing Category in the Chromeleon Chromatography Studio window Go to the Data Processing Home tab Either e Select a preset work area layout which contains a calibration pane from the Presets group OR e Select Calibration Plot in the Panes group Figure 8 Page 32 Quick Start Guide Chromeleon 7 Tyr External UN ME 0 00 0 13 0 25 0 38 0 50 0 63 0 75 0 88 1 00 1 13 1 20 Figure 8 A Calibration Curve Tip You can view the calibration curve for each component of a multi component standard by double cl
36. ner In the Report Designer category you can view reports and edit report templates The Navigation Pane shows a list of all channels injections and report templates available in the sequence In the Work Area you can view and modify the report 3 3 2 5 Electronic Report In the Electronic Report category you can create and manage electronic reports This is an electronically captured snapshot of the results The Navigation Pane shows a list of all injections and sheets available in the electronic report and the electronic report itself The Work Area shows the electronic report or when no electronic report is available the option to create one Quick Start Guide Page 61 Chromeleon 7 3 3 2 6 UV Spectral Library The UV Spectral Library view of the Chromatography Studio provides tools for managing and comparing spectra extracted from 3D Field data 3 3 2 7 Menus Chromeleon 7 Studio commands are accessible via the Ribbon or Studio Menu To access the Studio Menu click the Chromeleon icon f Page 62 Quick Start Guide Index Acquiring Data 14 37 Administration Console 47 Blank 55 Calibration 30 Calibration Curves 32 Calibration Levels 31 Calibration Standard 31 55 Category Bars 52 58 Check Standard 55 Chromatogram 19 Client 47 50 Cobra 21 23 Component Table 27 29 42 43 Confirming Peak 46 Connect 6 Console 4 50 51 Data Processing 17 60 Data Vault 53 54 Data Vault Manager 48 Detection Parameters
37. ogram by clicking somewhere in the chromatogram plot area Click the Processing tab and activate the Cobra Peak Detection Wizard by selecting the Cobra Wizard Y in the Detection Parameters group The Cobra Wizard opens Select the area of the chromatogram to be integrated If the section selected contains negative peaks for example solvent peaks you can specify that these are ignored during Quick Start Guide Page 21 Chromeleon 7 Cobra Peak Detection by checking the Consider Void Peak check box Otherwise leave this check box cleared Click Next 5 Choose one of the following possibilities to define a range in order to determine baseline noise e Select the Use Auto Range option default which calculates a suitable time range OR e Manually enter a baseline Click Next 6 Choose one of the following possibilities for smoothing chromatographic data e Select the Use Auto Smoothing Width option default for automatically smoothing data OR e Select the narrowest peak in the chromatogram in order to define the Cobra smoothing width used for peak detection Click Next 7 Choose one of the following possibilities to define the peak area threshold which determines the minimal peak area Any peaks whose area is below this threshold will be ignored during detection or integration e Select the Use Auto Minimum Area default option which automatically calculates a minimum area OR
38. omponent Table tab 4 Click the Click here to add a new component link at the bottom of the component table A Create new Component dialog box opens 5 Type the name of the component in the Name field and click Create A new component is created and diplayed in the component table 6 Update the component retention time and window in the Ret Time and or Window columns of the component table Quick Start Guide Page 29 Chromeleon 7 Tip Over a period of time peak retention times may drift from their expected values Because of this it is sometimes useful to set wide peak windows in the component table When peak retention time drift is too large for this method to compensate you can use the retention time of a previous peak for peak identification For details on correcting for Retention Time drift see Identify Peaks in the Chromeleon Help 2 6 4 2 Modifying Retention Times and Windows You can modify the retention time and width of the peak window by modifying the properties in the component table or by dragging the peak window on the chromatogram plot 2 6 5 Calibration and Quantitation In order to convert the area below a peak or the peak height into absolute amount or concentration values calibration is required before the analysis The calibration coefficients obtained during calibration can then be used to calculate unknown amounts This section takes you through the steps required to perform a simple external st
39. or dependent of the chromatogram plot The basic functionality is described in this section Quick Start Guide Page 37 Chromeleon 7 2 8 3 1 MS Plot The MS Plot can be enabled by clicking the Ju Mass 5 in the Panes group of the Data Processing Home tab Figure 9 Apex Peak 75 Scan 518 RT 2 31 min NL 1 00E 008 FTMS p ESI Full ms 200 00 700 00 338 34052 283 26257 524 37024 Figure 9 Mass Spectra Plot To display spectra the user is required to select one of the following e A peak from the chromatogram e Acomponent from the navigation pane OR e A data point using the Time Spectra Tool in the Peak Purity group on the Layout tab page of the Data Processing Category Plot Mode MS data can be acquired in either profile continuous or centroid discrete mode Profile data can be algorithmically converted to centroid format but centroid to profile is not possible Select a mass spectra plot to display the Spectral Plot Tools ribbon Then click the Layout tab To view data in centroid mode click the Page 38 Quick Start Guide Chromeleon 7 Centroid radio button in the Plot Mode group or Automatic in order to view all data as it was originally acquired SE In order to view supplemental spectra click cted ly Background oy la Reference jn the Overlays group The Overlays group is equal to the Plot Mode on the Layout tab page on the Spectral Plot Tools ribbon Click Reference to
40. ore information Page 46 Quick Start Guide Chromeleon 7 3 Appendix Chromeleon Overview 3 1 Introduction Chromeleon is a Chromatography Data System that allows you to control chromatography instruments and evaluate process report and backup data Chromeleon has several software components Instrument Controller Service The Instrument Controller Service handles communication with and data acquisition from the connected instruments Client The Chromeleon Client provides the user interface for all tasks related to instrument operation data analysis and data management Services Manager Shows the status of the Chromeleon Instrument Controller Service and provides a user interface to control this service The status of all other Chromeleon services is also displayed Instrument Configuration Manager Allows configuration of instruments connected to the Instrument Controller PC Administration Console Central access point for administrative tasks like e License Manager Provides tools for managing licenses for Chromeleon stations and users e Scheduler Provides tools for scheduling data transfer Quick Start Guide Page 47 Chromeleon 7 e User Database Provides tools for managing system policies users and roles access privileges and operational privileges e Global Policies Provides settings for global Chromeleon policies e Discovery Central repository containing information about the available ins
41. re sequence follow the steps for Printing Results for a Single Injection but in the Print dialog box e Select Apply to Current Sequence e When selecting the Sheets to be printed you can click the Down Arrow in the Condition column to apply print conditions for the selected sheet Tip To print several injections from a sequence first select the injection row or rows you want to print right click and then click Print Page 36 Quick Start Guide Chromeleon 7 2 8 MS in Chromeleon MS instrument control and data visualization processing support are provided starting in Chromeleon 7 2 Many of the features that can be used for LC IC and GC analysis can be used for MS analysis This section describes the features which are unique to MS 2 8 1 MS Instrument Control Direct instrument control is governed by the MS driver and external program provided with the MS hardware Please refer to the User Manual provided for your specific MS model for instructions on how to use the external program 2 8 1 1 Creating an MS Instrument Method Please refer to the User Manual provided with your specific hardware 2 8 2 Acquiring Data with an MS Data acquisition with an MS after an MS instrument method is created is identical to data acquisition with non MS instrument configurations Please refer to section 2 5 for more details 2 8 3 MS Data Visualization MS data visualization can be done with the spectral plot independent
42. rkflows eWorkflows are electronic procedures for automating laboratory processes related to a chromatographic analysis An eWorkflow contains a set of templates such as instrument methods processing methods report templates view settings and or spectral libraries and a set of rules The rules define for example the sequence layout such as the maximum number of Unknown injections allowed between Calibration Standards and the list of instruments in the network that are suitable for the analysis When you start an eWorkflow it will create a sequence with predefined associated files and a well defined structure The list of available eWorkflows is visible in the Navigation Pane An overview of the instruments including their status that can be used with the selected eWorkflow is displayed in the Work Area From here you can launch an eWorkflow and will be guided in creating an appropriate sequence Page 56 Quick Start Guide Chromeleon 7 3 3 2 Chromatography Studio In the Chromatography Studio you can edit all objects related to the selected sequence e Injection List e Instrument Methods e Processing Methods e View Settings e Report Templates e Electronic Reports e Spectral Libraries When you open a sequence from the Console the Chromatography Studio Figure 20 is opened Note When you open an object outside the context of a sequence only the corresponding category of the Studio is available Quick Start Gu
43. rough the objects available in the selected category e Work Area The content changes according to the selected category There are two additional parts for user interaction e Ribbon The menu tool for main commands in the Studio Commands are organized in groups which are collected together under tabs To reduce clutter some tabs are only shown when needed e Studio Menu To access the Studio Menu click the Chromeleon icon in the top left corner of the Chromatography Studio window From this menu you can access general tasks such as printing exporting and saving 3 3 2 1 Injection List When the Injection List category is selected you can edit print and export the injection list The Navigation Pane gives an overview of all files used in the sequence The Work Area displays further details about each Quick Start Guide Page 59 Chromeleon 7 injection such as the type of sample for example Calibration Standard and the injection status Note You can also edit the injection list directly in the Console If a sequence is open in both the Console and the Studio changes made in either window are automatically made in the other so that copies of the sequence stay synchronized 3 3 2 2 Instrument Method When the Instrument Method category is selected you can edit instrument methods The Navigation Pane lists the instrument methods in the sequence and provides an overview of the instrument s modules The Wor
44. te Chromeleon 6 Datasources ES are visible in Chromeleon 7 It is not possible to make changes in these Datasources but data can be copied from them to Chromeleon 7 Data Vaults Quick Start Guide Page 53 Chromeleon 7 Data can be accessed and organized from the Navigation Pane The Work Area shows the content of the selected object and allows you to edit the object A Data Vault can contain the following objects Folder A container for objects Use folders to organize data in a Data Vault pi Sequence A collection of injections that belong together A typical sequence contains an instrument and processing method a report template and a view settings file lal Instrument Method A collection of timed commands for an instrument to perform during a chromatographic analysis d A Processing Method A collection of parameters including parameters for peak detection and calibration which are used when evaluating chromatograms El Report Template A file which defines how data is displayed printed or exported A report template can also contain calculations When applied to a sequence to view print or export the results the outcome is referred to as a report Electronic Report An electronic version of the results of a sequence View Settings The definition of how data is presented on the screen UV Spectral Library A collection of spectra used for peak identification Sp Query A Data Vault search Page 54
45. titation XIC If there are currently no XICs defined the MS Quantitation Page 42 Quick Start Guide Chromeleon 7 Peak tab page is added Otherwise an MS Confirming Peak tab page is created In order to assist you define additional detection parameters Chromeleon displays the mass spectrum at the specified retention time Note that no mass spectrum might exist at the exact retention time In this case the MS Quantitation Peak tab will show the nearest spectrum to the defined retention time from the XIC Properties General Extracted lon Chromatograms ee Extraction Window Evaluati oe Use Retention Time 1 410 min Use Retention Window 0 500 AG Calibration i Specify Time 0 000 min Specify Window 0 100 min JUL MS Quantitation Peak TIC x ki gt Signal No data points forthe Eg current filter withinthe PS extraction window Mass Range D Precursor Mass XIC Mass es or Range s Filter Smoothing Points Default None el 3 C Use default MS Detection settings 1205 4 1004 279 16 907 391 28 2 Desloratadine d4 Figure 14 Extracted lon Chromatograms property page 3 Inthe Type field select the appropriate selection Quick Start Guide Page 43 Chromeleon 7 a TIC Typically used for processing of acquisition of non multiplexed SIM or SRM experiments b Mass Range Typically used for processing of Full Scan experiments Note If
46. truments and Data Vaults e Local Machine Provides tools for managing local Chromeleon 7 Data Vaults Create Mount and Dismount and Chromeleon 6 Datasources Mount and Dismount and enables you to change the Chromeleon Domain Controller Page 48 Quick Start Guide Chromeleon 7 3 2 Instrument Controller Service The Chromeleon Instrument Controller Service handles all real time instrument processes communications control and data acquisition It runs in the background as a Windows service on PCs to which instruments are physically connected Its status is represented by an icon a E in the Notification Area of the Windows Taskbar Figure 17 H E Customize 18 36 D P Jha e 05 07 2013 B i 18 32 Sekt 05 07 2013 Figure 17 Notification Area of Windows Taskbar for Windows XP and Windows 7 You can add configure or delete instruments and modules connect to instruments and track changes made to instruments from the Instrument Configuration Manager Quick Start Guide Page 49 Chromeleon 7 3 3 Chromeleon Client The Chromeleon Client provides the user interface for all tasks related to instrument operation data analysis and data management The Chromeleon Client contains two windows Chromeleon Console Chromatography Studio Page 50 The main Chromeleon window in which you can control instruments navigate through all data and use or manage eWorkflows A separ
47. uick Start Guide Page 17 Chromeleon 7 3 Open the Data Processing Category and in the Navigation Pane select the injection you want to view The data for that injection is displayed in the Work Area using the default preset view Tip There are several views in Chromeleon which can be selected from the Presets group on the Data Processing Home tab You can also create new views and store these to be used again See Create New View Settings in the Chromeleon Help for details on setting up custom views 4 Youcan navigate through the data by e Using the buttons in the Navigation group of the Data Processing Home tab e Selecting injections channels or components in the Navigation Pane OR e Double clicking a component or injection in the Integration or Summary table in the Interactive Results pane Figure 4 Page 18 Quick Start Guide Chromeleon 7 A B c D E F Calibration Standard D io e D y A PAL o lt el Del Le 3 W 2 3 cal_std_20 Calibration Standard 4 0 4 3 44 4 cal_std_50 Calibration Standard 41 44 n a 5 cal_std_100 Calibration Standard 41 44 n a 6 matrix_blank Unknown 41 4 3 ER 7 qc_std_50 Unknown 41 44 n a 8 solvent_blank Unknown na n a n a 9 unknown1 Unknown 4 0 44 n a 10 unknown2 Unknown 41 44 na 11 unknown3 Unknown 41 44 Summa MS Device Information A Peak Results Library Search A Sy Figure 4 Selection in Interactive Results table This section covers e
48. vice handles instrument communications control and data acquisition It runs in the background as a Windows service on any PC to which instruments are physically connected Its status is represented by an icon in the Notification Area of the Windows taskbar Figure 1 H E Customize SC Seen 18 32 _ He oe 05 07 2013 Figure 1 Notification Area of Windows Taskbar for Windows XP and Windows 7 2 lt Instrument Controller Service is stopped go Instrument Controller Service is running Quick Start Guide Page 5 Chromeleon 7 If the Instrument Controller Service is stopped start it by following these steps 1 Right click the Chromeleon tray icon in the notification area of the Windows taskbar 2 Click Start Chromeleon Instrument Controller Tip If the Chromeleon tray icon is not visible on the taskbar click Start point to Programs or All Programs depending on the operating system open the Chromeleon 7 folder and click Services Manager Note You can configure the Chromeleon Instrument Controller Service to automatically start every time the computer is switched on See the Controlling Instruments and Modules section of the Chromeleon Help for more information 2 3 2 Establishing a Connection Before you can control an instrument communication must be established between the modules and the Chromeleon Instrument Controller This is referred to as Connecting the Modules To connect the modules
49. view additional options to select the desired reference spectrum Some of the overlay functions for example the Background overlay require relevant settings to be defined in the processing method Extracted lon Chromatogram XIC When chromatographic MS data is acquired this is displayed as a Total lon Chromatogram TIC which is created by summing all mass peaks for each data point In order to increase specificity for a component and to reduce background noise contribution an XIC is created An XIC can be created in two manners e Left clicka mass peak in the mass spectrum when the an cursor appears OR e Right click a mass peak in the mass spectrum and select Extract lon Chromatogram from the context menu The Extract MS Channel dialog box opens Figure 10 Quick Start Guide Page 39 Chromeleon 7 Extract MS Channel x Trace Mass Range ia Filter None Mass range s 360 00000 370 00000 m z Smoothing None y Channel name MS_ 360 00000 370 00000 _ Cancel _ Figure 10 Extract MS Channel dialog box Both actions will result in a new chromatographic channel being created from the selected mass to charge ratio or range 2 8 4 MS Data Processing Processing Method The basic principles behind MS data processing are similar to data processing of non MS data The differences for MS will be covered in this section Please refer to section 2 6 for general information on data processing In order to disp
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