Agilent MassHunter Workstation Software

Agilent MssHunter Worksttion Softwre Qulittive Anlysis Fmiliriztion Guide for GC/MS Agilent Technologies

Notices Agilent Technologies, Inc. 2012 No prt of this mnul my e reproduced in ny form or y ny mens (including electronic storge nd retrievl or trnsltion into foreign lnguge) without prior greement nd written consent from Agilent Technologies, Inc. s governed y United Sttes nd interntionl copyright lws. Mnul Prt Numer G3336-90134 Edition Revision A, April 2012 Printed in USA Agilent Technologies, Inc. 5301 Stevens Creek Blvd. Snt Clr, CA 95051 USA Microsoft, Windows 7, nd Excel re U.S. registered trdemrk of Microsoft Corportion in the US nd/or other countries. Softwre Revision This guide is vlid for B.05.00 nd lter revisions of the Agilent MssHunter Worksttion Softwre - Qulittive Anlysis progrm, until superseded. Wrrnty The mteril contined in this document is provided s is, nd is suject to eing chnged, without notice, in future editions. Further, to the mximum extent permitted y pplicle lw, Agilent disclims ll wrrnties, either express or implied, with regrd to this mnul nd ny informtion contined herein, including ut not limited to the implied wrrnties of merchntility nd fitness for prticulr purpose. Agilent shll not e lile for errors or for incidentl or consequentil dmges in connection with the furnishing, use, or performnce of this document or of ny informtion contined herein. Should Agilent nd the user hve seprte written greement with wrrnty terms covering the mteril in this document tht conflict with these terms, the wrrnty terms in the seprte greement shll control. Technology Licenses The hrdwre nd/or softwre descried in this document re furnished under license nd my e used or copied only in ccordnce with the terms of such license. Restricted Rights Legend U.S. Government Restricted Rights. Softwre nd technicl dt rights grnted to the federl government include only those rights customrily provided to end user customers. Agilent provides this customry commercil license in Softwre nd technicl dt pursunt to FAR 12.211 (Technicl Dt) nd 12.212 (Computer Softwre) nd, for the Deprtment of Defense, DFARS 252.227-7015 (Technicl Dt - Commercil Items) nd DFARS 227.7202-3 (Rights in Commercil Computer Softwre or Computer Softwre Documenttion). Sfety Notices CAUTION A CAUTION notice denotes hzrd. It clls ttention to n operting procedure, prctice, or the like tht, if not correctly performed or dhered to, could result in dmge to the product or loss of importnt dt. Do not proceed eyond CAUTION notice until the indicted conditions re fully understood nd met. WARNING A WARNING notice denotes hzrd. It clls ttention to n operting procedure, prctice, or the like tht, if not correctly performed or dhered to, could result in personl injury or deth. Do not proceed eyond WARNING notice until the indicted conditions re fully understood nd met. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS

In This Guide This guide contins informtion to lern to use your Agilent MssHunter Worksttion Softwre - Qulittive Anlysis with GC/MS dt. Before you egin the exercises, plese red the instructions in Before you egin these exercises..." on pge 5. Exercise 1 Exercise 2 Exercise 3 Lern sics of qulittive nlysis In this exercise, you explore some of the mny powerful cpilities of the Qulittive Anlysis progrm. These tsks re importnt no mtter wht dt type you re using. Find nd identify In the first two sets of tsks, you find nd identify low-concentrtion sulf drugs within complex mtrix nd generte their formuls for oth TOF nd Q-TOF dt. You lso do moleculr feture extrction on protein digest with oth TOF nd Q-TOF dt. These tsks cn lso e performed on Triple Qud dt. Use workflows, export nd print In these tsks, you lern to set up nd run ny qulittive nlysis method. You lso lern to edit method to utomte the nlysis nd/or compound identifiction. Then you run the ctions within the utomted method when you open dt file. You lso lern to crete method to perform utomted ctions with worklist. Ech of these tsks is done using different workflow. Reference In this chpter, you lern some sics out the Qulittive Anlysis progrm. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 3

Wht s New in B.05.00 Service Pck 1 The GC/Q-TOF Compound Screening workflow is ville. The Qulittive Anlysis progrm supports GC/Q-TOF dt. Some of the lgorithms tht cn e used with GC/Q-TOF dt re the Find Compounds y Chromtogrm Deconvolution, Find Compounds y Trgeted MS/MS lgorithm, the Find Compounds y Formul lgorithm, nd the Generte Formuls from MS Peks lgorithm. You cn generte formuls from MS peks for n entire MS user spectrum. The softwre supports Indexed Dt Access (IDA) which improves the performnce of Find y Chromtogrm Deconvolution. The Agile integrtor is updted. A script is dded to extrct ll non-ms chromtogrms. A script is dded to extrct ll instrument curves. You cn now export CEF file contining ccurte mss informtion. in B05.00 (Qulittive Anlysis) Qulittive Anlysis is supported on Windows 7 Professionl (64 it) only. Reviewing of compound results is fster. Extrcting MS profile spectr nd EIC is fster. Extrcting multiple MS EIC (centroid nd profile) is fster. Finding compounds using the Find y Formul lgorithm is fster. You cn mnully extrct Find y Formul compound. You cn specify in the method how mny compounds to report for ech compound. You cn specify in the method to utomticlly increse the numer of mtches reported for isomeric compounds. 4 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS

Before you egin these exercises... You cn specify in the method to only generte compounds for mtched formuls. You cn specify to give wrning or error for Find y Formul compound if the Score is less thn the entered vlue. You cn specify to give wrning or error for Find y Formul compound if second ion is expected nd not found, nd the undnce of the second ion is supposed to e greter thn or equl to the vlue entered. You cn specify the contriution to the overll Score tht the Retention time score mkes. You cn specify to use oth the MS spectrum with ckground spectrum sutrcted nd the MS spectrum with no ckground spectrum sutrcted. The est result is returned. You cn either export only the highlighted results or ll results when exporting CEF file. You cn extrct n MS/MS spectrum either for ech collision energy or n verge MS/MS spectrum for ll collision energies. Instll the softwre. See the Instlltion Guide for instructions. Copy the folder nmed Dt from your instlltion disk in uncompressed formt to ny loction on your hrd disk. This folder contins ll the dt files needed for these exercises. You my need to first extrct the dt files from their.zip formt. NOTE Do not reuse the exmple dt files lredy on your system unless you know tht you copied them from the originls on the disk nd you re the only one using them. If the exmple dt files lredy on the system do not mtch the originl ones on the disk exctly, then the results otined during these exercises will not mtch those shown in the guide. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 5

6 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS

Contents Exercise 1 Lern sics of qulittive nlysis 9 Tsk 1. Open the Qulittive Anlysis progrm 10 Tsk 2. Configure User Interfce for GC/MS dt 12 Tsk 3. Zoom in nd out of the chromtogrm 15 Tsk 4. Anchor chromtogrm 17 Tsk 5. Chnge window lyouts 18 Tsk 6. Extrct chromtogrms 20 Tsk 7. Interctively integrte GC/MS chromtogrm 22 Tsk 8. Clculte System Suitility vlues 27 Tsk 9. Extrct spectr from chromtogrm 30 Tsk 10. Add nnottions 39 Tsk 11. Add mss cliper 43 Exercise 2 Find nd identify 45 Tsk 12. Find compounds y chromtogrm deconvolution 45 Tsk 13. Identify compounds using the Serch Lirry lgorithm 49 Tsk 14. Find compounds y MRM (MRM only) 52 Tsk 15. Generte formuls nd serch lirry for pek spectr 55 Tsk 16. Sve results 60 Exercise 3 Use workflows, export nd print 65 Tsk 17. Set up nd run qulittive nlysis method using the generl workflow 66 Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow 71 Tsk 19. Export CEF file 74 Tsk 20. Print n nlysis report 75 Tsk 21. Print compound report 78 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 7

Contents Reference 81 Work with windows 82 Work with result dt in Dt Nvigtor 84 Perform opertions on the chromtogrm 85 Perform opertions on n MS or MS/MS spectrum 86 Work with chromtogrphic visul dt 87 Work with spectrl visul dt 88 Workflows 89 Customize report templte 93 8 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Agilent MssHunter Worksttion Softwre Qulittive Anlysis Fmiliriztion Guide for GC/MS Exercise 1 Lern sics of qulittive nlysis Tsk 1. Open the Qulittive Anlysis progrm 10 Tsk 2. Configure User Interfce for GC/MS dt 12 Tsk 3. Zoom in nd out of the chromtogrm 15 Tsk 4. Anchor chromtogrm 17 Tsk 5. Chnge window lyouts 18 Tsk 6. Extrct chromtogrms 20 Tsk 7. Interctively integrte GC/MS chromtogrm 22 Tsk 8. Clculte System Suitility vlues 27 Tsk 9. Extrct spectr from chromtogrm 30 Tsk 10. Add nnottions 39 Tsk 11. Add mss cliper 43 In this exercise, you explore some of the mny powerful cpilities of the Qulittive Anlysis progrm for working with GC/Q-TOF nd GC/QQQ dt. Ech exercise is presented in tle with three columns: Steps Use these generl instructions to proceed on your own to explore the progrm. Detiled Instructions Use these if you need help or prefer to use step-y-step lerning process. Comments Red these to lern tips nd dditionl informtion out ech step in the exercise. Agilent Technologies 9

1 Lern sics of qulittive nlysis Tsk 1. Open the Qulittive Anlysis progrm Tsk 1. Open the Qulittive Anlysis progrm In this tsk you open multiple dt files using the current method. Tsk 1. Open the Qulittive Anlysis progrm with multiple dt files Steps Detiled Instructions Comments 1 Open the Qulittive Anlysis progrm. Open the dt files, Pest - 200 - Scn.d, Pest - STD 200 MRM.d, Pest Strw-01 SPIKED 1 pp - 1 ul inj.d nd MSD_mix_4stds_DG_spl200_0 3.d in the folder \\MssHunter\Dt, or in the folder where you copied them. Doule-click the Agilent MssHunter Qulittive Anlysis B.05.00 icon. The system displys the Open Dt Files dilog ox. Go to the folder \\MssHunter\ Dt\GC or the folder where the exmple files re locted. The Pest - 200 - Scn.d file contins MS dt, nd the Pest - STD 200 MRM.d nd Pest Strw-01 SPIKED 1 pp - 1 ul inj.d files contin oth MS nd MS/MS dt (ll GC/QQQ). MSD_mix_4stds_DG_spl200_03.d contins GC/Q-TOF dt. You cn get help for ny window, dilog ox, or t y pressing the F1 key when tht window is ctive. Mke sure tht the Use current method utton is clicked. Mke sure tht the Lod result dt check ox is cler. If the Lod result dt check ox is not ville, then no results hve een sved in the dt file. You lern how to sve results in Tsk 16. Sve results on pge 60 for instructions on how to sve results. Mke sure tht the Run File Open ctions from selected method check ox is cler. Figure 1 Open dt files when opening softwre 10 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 1. Open the Qulittive Anlysis progrm Tsk 1. Open the Qulittive Anlysis progrm with multiple dt files (continued) Steps Detiled Instructions Comments c d Press nd hold the Shift key while you click Pest - 200 - Scn.d, Pest - STD 200 MRM.d, Pest Strw-01 SPIKED 1 pp - 1 ul inj.d nd MSD_mix_4stds_DB_spl200_03.d. Click Open. All four dt files re displyed in the Dt Nvigtor window, nd 1 to 3 chromtogrms re displyed in the Chromtogrm Results window. e Click the List Mode icon in the Chromtogrm Results toolr. If you press the Ctrl key, you cn pick files which re not directly next to ech other in the list. Wht you see in the min window t this point depends on the method, lyout, disply nd plot settings used efore you opened these files. When you click the List Mode icon, the ckground of the icon chnges to ornge. Mximum Numer of List Pnes icon Disply Options icon You click the X utton to close this window. Figure 2 Qulittive Anlysis min window with the GC/Q-TOF Compound Screening Workflow loded. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 11

1 Lern sics of qulittive nlysis Tsk 2. Configure User Interfce for GC/MS dt Tsk 2. Configure User Interfce for GC/MS dt In this tsk, you switch to either the Generl workflow (for GC/QQQ customers) or the GC/Q-TOF Compound Screening workflow (for GC/Q-TOF customers). These two workflows re the only workflows tht support nlyzing GC/MS dt. Then, you open the User Interfce Configurtion dilog ox nd mrk the pproprite check oxes for GC/QQQ system or GC/Q-TOF system. Tsk 2. Configure User Interfce for GC Steps Detiled Instructions Comments 1 Open the Qulittive Anlysis progrm. Doule-click the Agilent MssHunter Qulittive Anlysis icon. The system displys the Open Dt Files dilog ox. Click Cncel in the Open Dt Files dilog ox. You cn get help for ny window, dilog ox, or t y pressing the F1 key when tht window is ctive. 2 Switch to either the Generl Workflow or the GC/Q-TOF Compound Screening Workflow. If you hve GC/QQQ instrument, click the Configurtion > Configure for Workflow > Generl commnd. If you hve GC/Q-TOF instrument, click the Configurtion > Configure for Workflow > GC/Q-TOF Compound Screening commnd. Click the Lod workflow s defult method utton nd the Lod workflow s defult lyout utton. c Click OK. d Click the List Mode icon in the Chromtogrm Results toolr. If the Dt Acquisition progrm for GC/QQQ or GC/Q-TOF is instlled on the sme computer, the softwre configures the User Interfce utomticlly. The GC/Q-TOF Compound Screening section my lredy e ville in the Method Explorer window. By defult, chromtogrms re overlid. For these exmples, the chromtogrms re shown in List Mode. 12 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 2. Configure User Interfce for GC/MS dt Tsk 2. Configure User Interfce for GC Steps Detiled Instructions Comments 3 If you hve GC/QQQ, configure the user interfce to show GC/QQQ fetures only. c d e f g h Click Configurtion > User Interfce Configurtion. Under Seprtion types, only mrk the GC check ox. If you hve GC/QQQ instrument, then under Ioniztion type, mrk the EI or other hrd ioniztion technique check ox, nd cler the CI, APCI, ESI, MADLDI or other soft ioniztion technique check ox. Under Mss ccurcy, cler the Accurte mss (TOF, Q-TOF) check ox. Mrk the Unit mss (Q, QQQ) check ox. Under Optionl softwre fetures, cler the Peptide Sequence Editor check ox nd the BioConfirm Softwre check ox. Under Non-MS detectors, cler the UV nd ADC check oxes. Mrk the Show dvnced prmeters check ox. Click OK. You chnge which commnds re ville in the User Interfce Configurtion dilog ox. If feture is not visile, it proly ws hidden when check ox ws clered in the User Interfce Configurtion dilog ox. Figure 3 Configuring the user interfce to use with GC/QQQ dt Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 13

1 Lern sics of qulittive nlysis Tsk 2. Configure User Interfce for GC/MS dt Tsk 2. Configure User Interfce for GC Steps Detiled Instructions Comments 4 If you hve GC/Q-TOF instrument, configure the user interfce to show GC/Q-TOF fetures only. c d e f g h i Click Configurtion > User Interfce Configurtion. Under Seprtion types, only mrk the GC check ox. Under Ioniztion type, mrk oth check oxes. Under MS levels, mrk oth check oxes. Under Mss ccurcy, mrk the Accurte mss (TOF, Q-TOF) check ox. Cler the Unit mss (Q, QQQ) check ox. Under Optionl softwre fetures, cler the Peptide Sequence Editor check ox nd the BioConfirm Softwre check ox. Under Non-MS detectors, cler the UV nd ADC check oxes. Mrk the Show dvnced prmeters check ox. Click OK. You chnge which commnds re ville in the User Interfce Configurtion dilog ox. If feture is not visile, it proly ws hidden when check ox ws clered in the User Interfce Configurtion dilog ox. Figure 4 Configuring the user interfce for GC/Q-TOF 14 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 3. Zoom in nd out of the chromtogrm Tsk 3. Zoom in nd out of the chromtogrm In this tsk, you ecome fmilir with the zoom in nd zoom out fetures of the Qulittive Anlysis progrm. Tsk 3. Zoom in nd out of the chromtogrm Steps Detiled Instructions Comments 1 Prctice zooming in nd out of only one of the three chromtogrms (oth x nd y xes). Hide the others. Zoom in twice on lst pek. Zoom in one more time utoscling the y-xis. Zoom out once to the previous zoom position. Completely zoom out to the originl chromtogrm. Cler the check oxes in the Dt Nvigtor window for the chromtogrms you wnt to hide. Click the right mouse utton nd drg over n re on the lst pek. Mke sure tht the Autoscle Y-xis during Zoom icon,, is not selected for this step. c Repet step. d Click the Autoscle Y-xis during e Zoom icon,, in the toolr. Click the right mouse utton gin nd drg over n re of the lst pek for the third time. The Qulity Anlysis progrm utomticlly scles the y-xis to the lrgest point in the rnge. f Click the Unzoom icon to undo the lst zoom opertion. You cn undo the lst fifteen zoom opertions. g Click the Autoscle X-xis nd Y-xis icon to zoom out completely. If line is not checked in the Dt Nvigtor window, tht informtion is not displyed in ny other window in the Qulittive Anlysis progrm. You simply mrk the check ox for tht informtion in the Dt Nvigtor window, nd the informtion is displyed in the other windows gin. You cn lso use these zoom fetures on spectr in the Spectrum Preview window, the MS Spectrum Results window nd the Difference Results window. A selected icon hs n ornge ckground color. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 15

1 Lern sics of qulittive nlysis Tsk 3. Zoom in nd out of the chromtogrm Tsk 3. Zoom in nd out of the chromtogrm (continued) Steps Detiled Instructions Comments 2 Prctice zooming in nd out on ech xis seprtely. Zoom in only long the x-xis. Hint: Right-click the x-xis vlues nd move cursor from left to right. Prtilly zoom out the x-xis. Hint: Move cursor in opposite direction. Completely zoom out of the x-xis. Repet the previous steps for the y-xis. To zoom in on the x-xis, move the cursor to the x-xis vlues until horizontl doule rrow ppers. Click the right mouse utton nd drg the new cursor from left to right cross the x-xis vlues. c To zoom out on the x-xis, click the right mouse utton nd drg from right to left on the x-xis vlues. d Click the Autoscle X-xis icon to completely zoom out on the x-xis. To zoom in on the y-xis, move the cursor to the y-xis vlues until verticl doule rrow ppers. Click the right mouse utton nd drg the new cursor from ottom to top c cross the y-xis vlues. To zoom out on the y-xis, click the right mouse utton nd drg from the top towrds the ottom of the y-xis vlues. d Click the Autoscle Y-xis icon to completely zoom out on the y-xis. Horizontl Doule Arrow New cursor ppers when you right-click the x-xis vlues. Verticl Doule Arrow New cursor ppers when you right-click the y-xis vlues. 16 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 4. Anchor chromtogrm Tsk 4. Anchor chromtogrm In this tsk, you nchor chromtogrm. When you nchor chromtogrm, the nchored chromtogrm remins permnently on disply s you scroll through the other chromtogrms to disply them. Tsk 4. Anchor chromtogrm Steps Detiled Instructions Comments Anchor chromtogrm. Show ll chromtogrms. Mke sure the chromtogrm viewing list is set to 1. In the Chromtogrm Results window, select the second TIC. Anchor this TIC. Scroll through the chromtogrms. Cler the nchor. c d e f In Dt Nvigtor mrk the check oxes for the chromtogrms you hid in the previous tsk. Mke sure the mximum numer of pnes is set to 1 in the Chromtogrm Results window. In the Chromtogrm Results window, select the second TIC. Right-click inside the chromtogrm, nd click Set Anchor. Use the scroll r in the Chromtogrm Results window to scroll through the list of chromtogrms. The second TIC stys visile lwys s the first chromtogrm. Click Chromtogrms > Cler Anchor. When you set n nchor for chromtogrm, n nchor icon ppers in the Dt Nvigtor window next to the nme of the nchored chromtogrm. Two chromtogrms pper in the Chromtogrm Results window fter you nchor one even though the viewing list sys 1. This now mens you view one chromtogrm in ddition to the nchored chromtogrm. You cn lso right-click the chromtogrm nd click Cler Anchor in the shortcut menu. Figure 5 Anchored TIC in the Chromtogrm Results window Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 17

1 Lern sics of qulittive nlysis Tsk 5. Chnge window lyouts Tsk 5. Chnge window lyouts In this tsk, you move windows within the min view nd crete vrious window lyouts. Tsk 5. Chnge window lyout Steps Detiled Instructions Comments 1 Chnge the window lyout: Chnge the window size. Sve window lyout. Unlock the lyout. Chnge the Chromtogrm Results window to e floting. Move the Chromtogrm Results window. Disply the tools for repositioning the windows. To chnge the size of window, drg the oundry etween the windows. To sve window lyout, click Configurtion > Window Lyouts > Sve Lyout. To unlock lyout, click Configurtion > Window Lyouts > Lock Lyout. To mke window flot, right-click the title r of the window, nd click Floting from the shortcut menu. To move window, click the title r of the window nd drg the window to the desired loction. To disply the repositioning tools, drg the window over one of the other windows. When one window is overlpped with nother, the progrm displys severl lyout tools, s shown in Figure 6. If the lyout is unlocked, the system does not disply check mrk next to the Lock Lyout menu. You cn only use the repositioning tools when the lyout is unlocked. You cn lso mke window flot y doule-clicking the title r of the window. The softwre hs mny different lyouts creted. You cn lso try loding different lyouts. The softwre hs severl different workflows. Ech workflow lods different lyout. Switching to different workflow lso chnges the lyout. Figure 6 Window repositioning tools 18 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 5. Chnge window lyouts Tsk 5. Chnge window lyout (continued) Steps Detiled Instructions Comments 2 Reposition the Chromtogrm Results window. Move the window so tht it is t the top, to the left, to the right nd then t the ottom of the other windows. Move two windows together so tht they re on top of one nother nd ville only through the ts t the ottom. Restore the defult lyout. If you drg the cursor over one of the smller icons, the window you re drgging will e plced ove, to the right, elow, or to the left of ll of the other windows. Drg the cursor over the lrger icon. The window cn lso e plced ove, to the right, elow, or to the left of the other window y drgging the cursor over the edges of the lrger icon. To t two windows together, drg the cursor over the center of the lrger icon. You will see shdow version of the two windows ted together. Stop drgging the mouse. The two windows will e ted together. Click Configurtion > Window Lyouts > Restore Defult Lyout. The cursor must e over one of the rrows in ox in order for repositioning to occur. Clicking the Restore Defult Lyout commnd restores the lyout tht is used with the Generl workflow nd the GC/Q-TOF Compound Screening workflow. If you re using different workflow, you need to lod the lyout tht is used with tht workflow. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 19

1 Lern sics of qulittive nlysis Tsk 6. Extrct chromtogrms Tsk 6. Extrct chromtogrms In this tsk, you extrct nd merge chromtogrms from the originl TIC. Tsk 6. Extrct chromtogrms Steps Detiled Instructions Comments 1 Extrct nd merge extrcted ion chromtogrms (EICs) from two msses in the Pest - 200 Scn.d dt file. The m/z vlues re 129.0 nd 414.2. Do not merge the peks from the individul msses into one chromtogrm. In the Dt Nvigtor window, cler the check oxes for the dt files except for Pest - 200 Scn.d. Open the Extrct Chromtogrms dilog ox, using the option elow or one of the options to the right: Click Chromtogrms > Extrct Chromtogrms. c In the List of opened dt files, click Pest - 200 - Scn.d. d In the Type list ox, select EIC. e In the m/z vlue(s) field, type 129.000, 414.200 f If necessry, cler the Merge multiple msses into one chromtogrm check ox to merge the EICs. g Click OK. h Set the Mximum numer of list pnes to 3 in the Chromtogrm Results toolr. You cn lso extrct chromtogrms in one of the following wys: Right-click inside the chromtogrm, nd click Extrct Chromtogrms. From Dt Nvigtor, highlight the TIC Scn for sulfs_posms.d, then right-click TIC Scn nd click Extrct Chromtogrms. You cn use n MS level of either All or MS. Note tht you cn lso choose to hve the extrcted chromtogrm utomticlly integrted fter extrction. You cn lso extrct chromtogrm from mss spectrum. Figure 7 The Extrct Chromtogrms dilog ox 20 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 6. Extrct chromtogrms Tsk 6. Extrct chromtogrms (continued) Steps Detiled Instructions Comments Figure 8 Merged extrcted ion chromtogrms (EICs) compred to the originl TIC Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 21

1 Lern sics of qulittive nlysis Tsk 7. Interctively integrte GC/MS chromtogrm Tsk 7. Interctively integrte GC/MS chromtogrm In this tsk, you lern different wys to integrte chromtogrm, chnge integrtion prmeters to modify the results nd clculte the Signl-to-Noise for the integrted peks for MS/MS dt. Tsk 7. Interctively integrte chromtogrm (GC/MS) Steps Detiled Instructions Comments 1 Integrte the TIC Scn chromtogrm for the Pest - 200 - Scn.d dt file, using ny of the options listed t right. 2 Disply only two chromtogrms t the sme time. Mrk the Pest - 200 - Scn.D line in the Dt Nvigtor window. Highlight the TIC Scn chromtogrm, nd use one of the following commnds: From the menu r click Chromtogrms > Integrte Chromtogrm. Right-click nywhere in the chromtogrm window, nd click Integrte Chromtogrm. In the Dt Nvigtor window, select Pest - 200 - Scn.D > User Chromtogrms > TIC Scn, then right-click the TIC Scn nd click Integrte Chromtogrm. Select 2 in the Mximum numer of list pnes ox in the Chromtogrm Results Toolr. Note tht the progrm integrted prcticlly ll the peks in the chromtogrm. You select the integrtor to use for MS dt, MS/MS dt, nd GC dt in the Method Editor window. This chromtogrm is n MS chromtogrm, so the vlues tht re set in the Integrte (MS) section of the Method Editor re used when integrting this chromtogrm. Mny smll peks re integrted. Figure 9 Integrted TIC Scn Chromtogrm with mny smll peks 22 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 7. Interctively integrte GC/MS chromtogrm Tsk 7. Interctively integrte chromtogrm (GC/MS) (continued) Steps Detiled Instructions Comments 3 Chnge the threshold to integrte fewer peks. Chnge the threshold to retin only the three lrgest peks. c d From the Method Explorer window, click Chromtogrm > Integrte (MS) to disply the Integrte (MS) t. Select the Agile integrtor. Click the Pek Filters t. Under Mximum numer of peks, mrk Limit (y height) to the lrgest, nd type 3. Note the lue tringle tht ppers when you chnge setting from the vlue sved in the current method. When you sve the method, the tringles dispper. Figure 10 Pek Filters t with Limit (y height) to the lrgest mrked 4 Reintegrte the chromtogrm e Click the utton on the Method Editor toolr to integrte using the new setting. Note tht only the three lrgest peks re now integrted. The pek t 2.491 hs higher height thn the pek t 16.858 minutes, so it is selected s the third pek. Figure 11 Integrted TIC Scn chromtogrm when limiting the numer of peks Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 23

1 Lern sics of qulittive nlysis Tsk 7. Interctively integrte GC/MS chromtogrm Tsk 7. Interctively integrte chromtogrm (GC/MS) (continued) Steps Detiled Instructions Comments 5 Integrte the TIC MRM chromtogrm for the Pest - STD 200 MRM.D dt file. In the Dt Nvigtor window, select the TIC MRM for the Pest - STD 200 MRM.d dt file. Use one of the following commnds to integrte the chromtogrms. From the menu r click Chromtogrms > Integrte Chromtogrm. Right-click nywhere in the chromtogrm window, nd click Integrte Chromtogrm. In the Dt Nvigtor window, right-click the highlighted chromtogrm nd click Integrte Chromtogrm. c Zoom in from 5.8 to 8.5 minutes. d Set the Mximum numer of list pnes to 2. Press the Ctrl key to highlight more thn one chromtogrm in the Dt Nvigtor window. Note tht the progrm integrted prcticlly ll the peks in the chromtogrm. These chromtogrms re MS/MS chromtogrms, so the vlues tht re set in the Integrte (MS/MS) section of the Method Editor window re used when integrting this chromtogrm. You cn select one integrtor to use to integrte MS chromtogrms nd different integrtor to use to integrte MS/MS chromtogrms. Figure 12 Integrted MRM chromtogrms 6 Select the MS/MS (GC) integrtor. Chnge the filter to only ccept peks with n solute height greter or equl to 20,000. c d e f From the Method Explorer window, select Chromtogrm > Integrte (MS/MS). Select MS/MS (GC) s the Integrtor. Click the Pek Filters t. Under Filter on, click Pek height. Under Height filters, mrk the Asolute height check ox. Type 20000 s the Asolute height. Note the lue tringle tht ppers when you chnge setting from the vlue sved in the current method. When you sve the method, the tringles dispper. 24 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 7. Interctively integrte GC/MS chromtogrm Tsk 7. Interctively integrte chromtogrm (GC/MS) (continued) Steps Detiled Instructions Comments Figure 13 Pek Filters t with Asolute height mrked 7 Reintegrte the chromtogrm g Click the utton on the Method Editor toolr. Note tht only the lrgest peks re now integrted. The smller peks t 6.2 minutes nd 6.8 minutes re not included in the integrtion results ny longer ecuse the solute height for ech of these peks is lower thn 20000 counts. Figure 14 Integrted TIC nd EIC MS/MS chromtogrms with higher threshold setting 8 Restore the settings tht re sved for the current method nd close Method Editor. Select the Chromtogrm > Integrte (MS/MS) section in the Method Explorer. Click the icon in the Method Editor. c Select the Chromtogrm > Integrte (MS) section in the Method Explorer. d Click the. icon in the Method Editor. e Close the Method Editor window. To cncel your chnges nd restore the vlues from the method tht is loded, click the Restore to lst sved vlues from file icon on the Method Editor toolr. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 25

1 Lern sics of qulittive nlysis Tsk 7. Interctively integrte GC/MS chromtogrm Tsk 7. Interctively integrte chromtogrm (GC/MS) (continued) Steps Detiled Instructions Comments 9 Delete ll chromtogrms except the originl. Delete the integrtion results from the originl chromtogrm. c d Under User Chromtogrms in the Dt Nvigtor window, highlight ll the chromtogrms except the originl. Right-click the highlighted chromtogrms, nd click Delete. Select ll of the TIC chromtogrms. Click Chromtogrms >Cler Results. When you use the Cler Results commnd, the chromtogrms re not deleted; the results tht re connected to the chromtogrms re removed. In this cse, the integrtion vlues re clered. 26 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 8. Clculte System Suitility vlues Tsk 8. Clculte System Suitility vlues In this tsk, you lern different wys to interctively integrte chromtogrm, chnge integrtion prmeters to modify the results nd view the signl-to-noise rtio for ech pek. You lso lern how to enle System Suitility clcultions. Tsk 8. Interctively integrte chromtogrm (MS) Steps Detiled Instructions Comments 1 Integrte the MSD_mix_4stds_DB_spl200_03.d nd Pest - 200 - Scn.d chromtogrm nd using ny of the options listed t right. Mrk the check ox next to the MSD_mix_4stds_DB_spl200_03.d dt file in the Dt Nvigtor window. Integrte the TIC Scn for these two files, using ny of the following options. From the min menu, click Chromtogrms > Integrte Chromtogrm. Highlight the chromtogrm. Then, right-click the chromtogrm, nd click Integrte Chromtogrm. In Dt Nvigtor, highlight the TIC Scn for oth dt files. Then, right-click either chromtogrm nd click Integrte Chromtogrm. For the Generl workflow, the integrtion uses the Generl Integrtor, ecuse tht is the integrtor selected in the method defult.m. For the GC/Q-TOF Compound Screening workflow, the integrtion uses the Agile Integrtor. You cn chnge this vlue in the Chromtogrm > Integrte (MS) > Integrtor t. Note tht the integrtion with defult prmeters is detecting very smll peks. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 27

1 Lern sics of qulittive nlysis Tsk 8. Clculte System Suitility vlues Tsk 8. Interctively integrte chromtogrm (MS) (continued) Steps Detiled Instructions Comments Figure 15 One of the shortcut menus in the Dt Nvigtor nd integrted chromtogrms 2 Enle system suitility clcultions for the MS chromtogrms. From Method Explorer, select Chromtogrm > Integrte (MS) to disply the Integrtor t. Click the Suitility t. Mrk Enle system suitility c clcultions. d Select the United Sttes Phrmcopoei (USP). e In the Column void time ox, type 1. f In the Column length ox, type 3000. Note the lue tringle tht ppers when you chnge setting from the vlue tht is sved in the current method. When you sve the method, the tringles dispper. The lgorithms tht re used to set severl of the columns in the Integrtion Pek List chnge, depending on the selected phrmcopoei. See the online Help for more informtion. The ctul column void time nd column length for these dt files is different thn these vlues. These re only used for this exmple. Figure 16 Chromtogrm > Integrte (MS) Suitility t 28 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 8. Clculte System Suitility vlues Tsk 8. Interctively integrte chromtogrm (MS) (continued) Steps Detiled Instructions Comments 3 Reintegrte the chromtogrm. Click the Integrte Chromtogrm icon on the Method Editor toolr to integrte using the new setting. 4 View the system suitility clcultions. Open the Integrtion Pek List window. Review the vlues for the noise region, nd clculte the signl-to-noise rtio for the integrted peks. c d Click View > Integrtion Pek List. Right-click the heder of the Peks window nd click Floting. Right-click the column heder of ny column tht you do not wnt to see nd click Remove Column. Right-click ny column heder nd click Add/Remove Columns to chnge the columns tht re visile. The system suitility clcultions re included in the Integrtion Pek List tle. These vlues include k, Tiling fctor, Pltes, Pltes/M, nd Symmetry. You cn lso enle system suitility clcultions for n MS, n MS/MS nd GC chromtogrm. Figure 17 Integrted Peks tle with system suitility vlues 5 Restore the settings for the defult method, nd close the Method Editor window nd the Integrtion Pek List window. c d To cncel your chnges nd restore the vlues from the defult method, click the Restore to lst sved vlues from file icon on the Method Editor toolr. Close the Method Editor window. Right-click the title of the Integrtion Pek List window nd click Floting. Click View > Integrtion Pek List. When you click the Floting commnd in the shortcut menu the second time, the Integrtion Pek List window is docked where it ws originlly. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 29

1 Lern sics of qulittive nlysis Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm In this tsk, you extrct spectrum from exctly where you specify in the chromtogrm. The Qulittive Anlysis progrm extrcts spectrum from specific dt point or extrct n verge spectrum from n verge of multiple dt points or rnges. Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments 1 Wlk chromtogrm to view the precursor ion nd product ion for the lst few peks of Pest - STD 200 MRM.d. Zoom in on the region etween 13 nd 16 minutes. Use the Wlk Chromtogrm icon. Review the spectr strting t out 13 minutes, nd move the rrow to the right. c d e f g h i j Mrk the Pest - 200 - MRM.D line in the Dt Nvigtor window. Close the Method Editor window. Close the MS Spectrum Results window. Click the TIC MRM chromtogrm in the Dt Nvigtor window. Click the Autoscle Y-xis during Zoom icon in the Chromtogrm Results toolr. Select 1 for the Mximum numer of list pnes. To zoom in on few peks, right-click the mouse ove the pek t 13 minutes nd drg it to 16 minutes, nd then relese. Click the Wlk Chromtogrm icon in the Chromtogrm Results toolr. Move the Wlk Chromtogrm cursor to ove the X xis t out 13 minutes, nd click. To nvigte from spectrum to spectrum, use the right nd left rrow keys on your keyord. The Wlk Chromtogrm tool is prticulrly useful on MS/MS dt for identifying precursor nd product ions. The spectrum for ech point you click in the Chromtogrm Results window is utomticlly displyed in the Spectrum Preview window, which is opened utomticlly. Sometimes, two spectr re displyed in the Spectrum Preview window. For exmple, two spectr re shown in the Spectrum Preview window for ech point you click ner the pek t 13.431 minutes. 30 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments Figure 18 Wlk chromtogrm to view the two MRM spectr for the pek t 13. 43 minutes Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 31

1 Lern sics of qulittive nlysis Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments 2 Extrct spectr on specific dt points for the pek t 5.2 minutes nd the pek t 14.3 minutes of the Pest - STD 200 MRM.d dt file. Extrct spectrum from the pek t or ner 5.2 min. nd then one of the vlleys, using ny one of the options descried under Comments. Extrct spectrum from the pek t or ner 14.3 minutes. (not the vlley yet) Chnge the disply to show t lest three spectr. Click the Rnge Select icon from the Chromtogrm Results toolr. Close the Spectrum Preview window. c Click the Zoom Out icon,, in the Chromtogrm Results toolr. d To zoom in to the pek t 5.2 minutes, right-click the mouse ove the pek t 4.0 min. nd drg it to 6.0 min., then relese. e On pek ner 5.2 min. extrct spectrum in ny of the wys listed in the Comments column. f On vlley ner 5.1 min., extrct the spectrum. g Click the Zoom Out icon,, in the Chromtogrm Results toolr. h Zoom into the region etween 14 nd 15 min. i On pek ner 14.3 minutes, extrct spectrum in ny of the wys listed in the Comments column. (Do not extrct the vlley spectrum yet.) j If necessry, select 4 in the Mximum numer of list pnes icon in the MS Spectrum Results toolr. When you zoom, mke sure the AutoScle Y-xis during Zoom icon, is on. The ckground of the icon is ornge when it is on. You cn extrct spectrum in ny of the following wys: Doule-click the dt point in the chromtogrm. Click the dt point in the chromtogrm, then right-click nywhere in the chromtogrm. Click Extrct MS Spectrum. The Extrct Spectrum dilog ox is displyed. Mke sure the Pest - STD 200 MRM.d file is selected, nd click Extrct in the Extrct Spectrum dilog ox. Note tht when you first extrct spectrum, the MS Spectrum Results window ppers contining the spectrum, nd the type of spectrum nd retention time pper under User Spectr. All susequent extrcted spectr pper in oth plces s well. When you extrct n MS spectrum from the pek ner 14.3 minutes, two spectr re extrcted ecuse two trnsitions occur t tht pek. 32 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments Figure 19 Min window with two MRM spectr from the pek t 5.2 minutes nd two MRM spectr from the pek t 14.3 minutes 3 Extrct n MS Spectrum for the vlley t 14.35 minutes of the Pest - STD 200 MRM.d dt file. Bring up Spectrum Preview. Extrct spectrum from the vlley t RT 14.3 minutes. Copy this spectrum to the User Spectr folder. Chnge the disply to show 6 spectr. Turn off Spectrum Preview. c d e Click the Spectrum Preview icon,. On vlley ner 14.3 minutes extrct spectrum. Right-click the spectrum in the Spectrum Preview window, nd click Copy to User Spectr. The spectr re copied to the User Spectr section in the Dt Nvigtor nd re shown in the MS Spectrum Results window. Click the down rrow next to the spectrum pne list, nd select 6. Close the Spectrum Preview window. When Spectrum Preview is enled, the system displys ny mnully-selected spectrum in the Spectrum Preview window ut not in the User Spectr section of Dt Nvigtor. With Spectrum Preview on, Qulittive Anlysis overwrites the previous spectrum when you extrct new spectrum. Spectrum Preview mode is useful when you quickly wnt to review the spectr in your chromtogrm nd sve only few of the spectr. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 33

1 Lern sics of qulittive nlysis Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments Figure 20 Chromtogrm Results nd MS Spectrum Results windows 4 Extrct spectrum tht verges ll points within specified rnge for the pek t 14.3 minutes for the Pest - STD 200 MRM.d dt file: Zoom out. Use the Rnge Select icon on the Chromtogrm toolr. Set the rnge cross the entire pek. Extrct the spectrum, using ny of the options listed. Click the Rnge Select icon on the Chromtogrm toolr. Click t the left side of the se of the pek t 14.3 minutes nd drg to the se of tht pek on the right. c Extrct the verge spectrum using one of the options on the right. d Select 2 in the Mximum numer of list pnes in the MS Spectrum Results window. You cn extrct n verge spectrum y doule-clicking the selected rnge in the chromtogrm. Or, right-click nywhere in the chromtogrm, nd click Extrct MS Spectrum from the shortcut menu. Note tht two verged MRM spectr pper. 34 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments Figure 21 Chromtogrm Results nd MS Spectrum Results showing two verged spectr 5 Extrct spectr tht verge the rnges of peks t 5.2 minutes nd t 14.3 minutes together for the Pest - STD 200 MRM.d dt file. Hint: Use the Rnge Select icon nd the Ctrl key to select the Pek 1 rnge tken from the hlfwy point. Extrct the spectr, using ny of the options on the right. Click the Zoom Out icon,, in the Chromtogrm Results toolr. Press the Ctrl key. c Click t the left side of the pek t 5.2 minutes nd drg to the right of tht pek, nd relese the mouse. d Relese the Ctrl key. e Extrct the verged spectr using this option or the one on the right: Doule-click inside the selected rnge in either pek. Rememer tht the second pek lredy hs rnge selected from step 4. To extrct spectr, you cn lso right-click nywhere in the chromtogrm nd clicking Extrct MS Spectrum. The Extrct Spectrum dilog ox is shown. Click Extrct. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 35

1 Lern sics of qulittive nlysis Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments The first spectrum hs trnsitions from oth time rnges. The second spectrum only hs one time rnge ecuse the 160.00 -> ** trnsition is not present in the pek t 5.2 minutes. Figure 22 Two verged spectr from two different rnges in the chromtogrm 6 Sutrct ckground spectrum every time you extrct pek spectrum from Pest - STD 200 MRM.d. Delete ny scns under User Spectr in Dt Nvigtor. Extrct ckground spectrum tht is the verge of spectrum t the strt of the pek nd spectrum t the end of the pek. Extrct pek spectrum from the integrted peks. Click the User Spectr line in the Dt Nvigtor. Right-click the User Spectr line, nd click Delete. Click Yes. c In Method Explorer, select Spectrum > Extrct (MS/MS). d Click the Pek Spectrum Extrction (MS/MS) t, if not visile. e In the Pek spectrum ckground MS/MS ox, select Averge of spectr t pek strt nd end. f In the Chromtogrm Results toolr, click the Pek Select icon,. g Click the Chromtogrms > Integrte commnd. h Select the pek t 5.206 minutes. i Right-click nd click Extrct Pek Spectrum from the shortcut menu. Note tht t the end of this process, ll extrcted pek spectr will utomticlly hve the designted ckground spectrum sutrcted. 36 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments Figure 23 Pek spectr with ckground pek spectrum sutrcted Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 37

1 Lern sics of qulittive nlysis Tsk 9. Extrct spectr from chromtogrm Tsk 9. Extrct spectr from chromtogrm Steps Detiled Instructions Comments 7 Integrte nd extrct pek spectr from the Pest - STD 200 MRM.d dt file. Click the TIC MRM chromtogrm in the Dt Nvigtor window. Click Chromtogrms > Integrte nd Extrct Pek Spectr. The pek spectr tht you extrcted mnully in the previous step is deleted utomticlly ecuse y defult the Cler previous pek spectr check ox is mrked in the Chromtogrms > Integrte (MS/MS) > Results t. Figure 24 Integrte nd Extrct Pek Spectr 8 Remove the integrtion results nd the pek spectr. Select the Pest - Std 200 MRM.d dt file. Click Chromtogrms > Cler Results > Include Pek Spectr. You cn insted click Chromtogrms > Cler Results > Only Chromtogrms if you do not wnt to delete the pek spectr. 38 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 10. Add nnottions Tsk 10. Add nnottions Tsk 10. Add n nnottion You cn dd n imge nnottion or text nnottion to the following grphics windows: Chromtogrm Results window MS Spectrum Results window If you sve the results for the dt file, nnottions re lso sved. Steps Detiled Instructions Comments 1 Select the MSD_mix_4stds_DG_spl200_03.d dt file. Hide the other chromtogrms. Mrk the check ox next to MSD_mix_4stds_DG_spl200_03.D in the Dt Nvigtor window. Click Edit > Show > Only Highlighted. The chromtogrms for the other dt files re utomticlly hidden. 2 Select the loction in the chromtogrm to dd text nnottion. c In the Chromtogrm Results window, click the Annottion tool ( )in the toolr. Move the cursor to the loction in the chromtogrm pne where you wnt to dd the nnottion. Right-click nd then click Add Text Annottion. The cursor chnges to cross-hir. You use this cursor to select the exct loction to dd the nnottion. The Annotte toolr is ville in the Chromtogrm Results window. You cn lso dd nnottions to the MS Spectrum Results window. 3 Add the informtion out the text nnottion in the Add/Edit Text Annottion dilog ox. c d e f Type the Text for the nnottion. Select the Text color. Select the Orienttion. Select the Font style nd Font size. Click either Anchored or Floting. If you click Anchored, select the options for the pointer to the text nnottion. If you click Floting, you cn chnge the reltive position. It is esier to chnge the position interctively in the grphics window. Click OK. You cn dd multiple nnottions to chromtogrm or spectrum. You cn use the icons in the Annotte toolr to select ll of the nnottions, delete nnottions nd edit nnottions. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 39

1 Lern sics of qulittive nlysis Tsk 10. Add nnottions Tsk 10. Add n nnottion (continued) Steps Detiled Instructions Comments The Annotte Toolr is only ville when the Annotte tool is selected. Figure 25 Add/Edit Text Annottion dilog ox nd the Chromtogrm Results window 4 Select the loction in the chromtogrm to dd the imge nnottion. Move the cursor to the loction in the chromtogrm pne where you wnt to dd the nnottion. Right-click nd then click Add Imge Annottion. You cn dd JPG or MOL imge file. 5 Add the informtion out the text nnottion in the Add/Edit Text Annottion dilog ox. c d e f Type the Text for the nnottion. Type 50 for the Scle width. Mrk the Lock spect rtio check ox. Click Floting. You cn chnge the reltive position. It is esier to chnge the position interctively in the grphics window. Click OK. Move the imge to the upper, right corner of the chromtogrm. The Agilent_Logo.tif file is included in the \\MssHunter\Report Templtes\Qul\B.05.00\en-US\ Letter folder. You need to convert it to JPG file. You cn dd multiple nnottions to chromtogrm or spectrum. 40 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 10. Add nnottions Tsk 10. Add n nnottion (continued) Steps Detiled Instructions Comments Figure 26 Add/Edit Imge Annottion dilog ox nd the Chromtogrm Results window 6 Zoom in to the first pek. Zoom to n re round the first pek t 5.5 minutes If n nnottion is nchored, it stys ttched t the position where it is nchored. If you zoom into different pek, n nchored nnottion my not e visile. If n nnottion is floting, then the nnottion is lwys shown in the sme position reltive to the upper left corner of the window. Figure 27 Add/Edit Imge Annottion dilog ox nd the Chromtogrm Results window Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 41

1 Lern sics of qulittive nlysis Tsk 10. Add nnottions Tsk 10. Add n nnottion (continued) Steps Detiled Instructions Comments 7 Switch ck to the Rnge Select tool in the Chromtogrm Results window. Delete the nnottion first. Click the icon to remove ll nnottions. Click the (Rnge Select) icon in the Chromtogrm Results toolr. If you wnt to sve the nnottions with the dt file results, see Tsk 16. Sve results on pge 60. You cn switch etween five different tools in the Chromtogrm Results toolr. Refer to the online Help for more informtion. The five tools re: Rnge Select Pek Select Mnul Integrtion Wlk Chromtogrm Annottion Mouse 42 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Lern sics of qulittive nlysis 1 Tsk 11. Add mss cliper Tsk 11. Add mss cliper A cliper shows the difference etween two points in spectrum. You cn dd cliper to the MS Spectrum Results window. If you sve the results for the dt file, clipers re lso sved. Tsk 11. Add mss cliper Steps Detiled Instructions Comments 1 Integrte nd extrct pek spectr from MSD_mix_4stds_DG_spl200_03.d. c d Mrk the check ox next to MSD_mix_4stds_DG_spl200_03.D in the Dt Nvigtor window. Click Edit > Show > Only Highlighted. Click Chromtogrms > Integrte nd Extrct Pek Spectr. Close the Method Editor window. 2 Add the cliper to the pek spectrum creted in the previous tsk. c d e In the MS Spectrum Results window, click the Delt Mss Cliper tool ( )in the toolr. (optionl) Select Profile Point to Point for the type of cliper in the Cliper toolr. Zoom in to 66 to 132 m/z. Move the cursor to the loction in the spectrum pne where you wnt to dd the cliper. Drg the cursor to the end point of cliper in the spectrum. As you drg the cursor, the vlue of the delt mss chnges. When you relese the mouse utton, the cliper is dded. The cursor chnges to n rrow. You use this cursor to select the strt nd end point of the cliper. You cnnot select the type of cliper if the spectrum is centroided ecuse Profile Point to Point hs no effect on centroid dt. The tringle cursor is set to the top of the pek tht is selected. 3 Modify the cliper to use different color. c d e f Click the cliper creted in the previous step. Click the Cliper Properties utton ( ) in the MS Spectrum Results Cliper toolr. (optionl) Type the Strt X nd Strt Y vlues. Select the Text color. Select the Font style nd Font size. Click OK. You cn dd multiple clipers to spectrum. You cn use the icons in the Cliper toolr to select ll of the clipers, delete clipers nd edit clipers. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 43

1 Lern sics of qulittive nlysis Tsk 11. Add mss cliper Tsk 11. Add mss cliper (continued) Steps Detiled Instructions Comments Figure 28 Delt Mss Cliper Settings dilog ox nd the MS Spectrum Results window 4 Delete integrtion results nd spectr. Click Chromtogrms > Cler Results > Include Pek Spectr. Click the Rnge Select tool. If you wnt to sve the clipers with the dt file results, see Tsk 16. Sve results on pge 60. 44 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Agilent MssHunter Worksttion Softwre Qulittive Anlysis Fmiliriztion Guide for GC/MS Exercise 2 Find nd identify Tsk 12. Find compounds y chromtogrm deconvolution 45 Tsk 13. Identify compounds using the Serch Lirry lgorithm 49 Tsk 14. Find compounds y MRM (MRM only) 52 Tsk 15. Generte formuls nd serch lirry for pek spectr 55 Tsk 16. Sve results 60 In these tsks, you find nd identify compounds in GC/MS dt files. Ech exercise is presented in tle with three columns: Steps Use these generl instructions to proceed on your own to explore the progrm. Detiled Instructions Use these if you need help or prefer to use step-y-step lerning process. Comments Red these to lern tips nd dditionl informtion out ech step in the exercise. Tsk 12. Find compounds y chromtogrm deconvolution This FindCompounds lgorithm identifies compounds in GC/MS dt nd cretes clened MS spectrum for ech compound. This functionlity is n esy wy to mine informtion from complex dt. You cn only use the Find Compounds y Chromtogrm Deconvolution lgorithm on GC/MS smple dt cquired in Scn, Product Ion scn or Neutrl Loss scn mode. Agilent Technologies 45

2 Find nd identify Tsk 12. Find compounds y chromtogrm deconvolution This tsk shows finding compounds y chromtogrm deconvolution with ccurte mss dt. You cn lso find compounds y chromtogrm deconvolution with unit mss dt fter you first chnge the extrction window. Tsk 12. Find compounds using Chromtogrm Deconvolution (GC/MS) Step Detiled Instructions Comments 1 Open the TIC for the MSD_mix_4stds_DG_spl200_03.d dt file. c If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DG_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox nd click Open. The Find Compounds y Chromtogrm Deconvolution lgorithm works with oth GC/QQQ nd GC/Q-TOF dt files. Figure 29 TIC chromtogrm from Pest - 200 - Scn.d 2 Configure the user interfce to work with GC dt. Follow the instructions in Tsk 2. Configure User Interfce for GC/MS dt on pge 12. For these exmples, lod the GC/Q-TOF Compound Screening workflow. 46 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 12. Find compounds y chromtogrm deconvolution Tsk 12. Find compounds using Chromtogrm Deconvolution (GC/MS) Step Detiled Instructions Comments 3 Find compounds using the chromtogrm deconvolution lgorithm. Select the Agile integrtor. Enter n SNR threshold of 20. Enter 100 ppm for the Left m/z delt nd Right m/z delt vlues. c d In the Method Explorer window, select Find Compounds > Find y Chromtogrm Deconvolution. On the Settings t under Pek filter, type 20 for the SNR threshold. Select PPM for the m/z delt units. Enter 100 for the Left m/z delt, nd enter 100 for the Right m/z delt. The Find y Chromtogrm Deconvolution section is lso ville in the GC/Q-TOF Compound Screening section. If you hve unit mss dt, you enter 0.3 AMU for the Left m/z delt vlue nd 0.7 AMU for the Right m/z delt vlue You cn extrct the complete result set for compound fter it is found y using the Compounds > Extrct Complete Result Set menu item when compound is highlighted. Figure 30 Settings t in the Find y Chromtogrm Deconvolution section Select to extrct EIC, MS spectr nd MS/MS spectr. e f Click the Results t. Mrk the Extrct EIC, Extrct ECC, Extrct clened spectrum nd Extrct rw spectrum check oxes. g Click to run the Find Compounds y Chromtogrm Deconvolution lgorithm on the dt file. h Click the View > Compound List commnd. The Qulittive Anlysis progrm finds 4 compounds under these conditions. If the dt file is not indexed, it cn tke long time when you run this lgorithm. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 47

2 Find nd identify Tsk 12. Find compounds y chromtogrm deconvolution Tsk 12. Find compounds using Chromtogrm Deconvolution (GC/MS) Step Detiled Instructions Comments 4 Exmine the compounds. See Figure 31 on pge 48. c d Select 2 in the Mximum numer of list pnes ox in the MS Spectrum Results toolr. Click the Hide Empty Columns icon in the Compound List window. Click the first compound in the Dt Nvigtor window. When the Dt Nvigtor window is selected, use the rrow keys to switch compounds. Showing oth spectr is convenient wy to disply ll the informtion for single compound. Note tht oth the clened spectrum nd the rw spectrum re shown. Figure 31 Find Compounds y Chromtogrm Deconvolution results 48 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 13. Identify compounds using the Serch Lirry lgorithm Tsk 13. Identify compounds using the Serch Lirry lgorithm In this tsk, you identify nd generte formuls for the compounds found in Tsk 12. Find compounds y chromtogrm deconvolution 45. You cn do this tsk if you hve purchsed the NIST08.l lirry or if you use the demo.l lirry. Tsk 13. Identify compounds using the Serch Lirry lgorithm Step Detiled Instructions Comments 1 Do lirry serch of ll of the compounds in the MSD_mix_4stds_DG_spl200_03.d dt file. c d e f g h i Highlight the compounds in the MSD_mix_4stds_DG_spl200_03.D dt file in the Dt Nvigtor window. In the Method Explorer window, click Identify Compounds > Serch Unit Mss Lirry. In the Settings t, click the utton. Select the demo.l lirry nd click the OK utton. Click Identify > Serch Lirry for Compounds from the min menu. You cn insted click the Serch Lirry for Compounds icon to run the lgorithm. Click View > Difference Results. Click View > Structure Viewer. Click View > Compound Identifiction Results, if necessry to disply this window. If necessry, click the t for the Compound Identifiction Results window. This window is ted with the Chromtogrm Results window. Click the Hide Empty Columns icon in the Compound Identifiction Results toolr. You cn lso click GC/Q-TOF Compound Screening > Identify y Lirry Serch in the Method Explorer. The sme section in the Method Editor window is displyed. Demo.l nd Nist08 should e instlled in the \MssHunter\ Lirry folder. Note tht mny of the compounds re identified fter serching the NIST08.l lirry. If you do not hve the NIST08.l lirry, select the demo.l lirry. You use the Lirry Editor progrm to modify lirries tht you use with the Serch Unit Mss Lirry lgorithm. This progrm is instlled with the Agilent MssHunter Quntittive Anlysis progrm. You click the icon to strt this progrm. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 49

2 Find nd identify Tsk 13. Identify compounds using the Serch Lirry lgorithm Tsk 13. Identify compounds using the Serch Lirry lgorithm Step Detiled Instructions Comments 2 Disply the Spectrl Lirry Results columns in the Compound List window nd the Compound Identifiction Results window. c d Click the Show Lirry Serch Columns utton ( ) in the Compound List toolr. Click the Hide Empty Columns utton ( ) in the Compound List toolr. Click the Show Lirry Serch Columns utton ( ) in the Compound Identifiction Results toolr. Click the Hide Empty Columns utton ( ) in the Compound Identifiction Results window. Figure 32 Compounds in MSD_mix_4stds_DG_spl200_03.D dt file nd the lirry serch results 50 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 13. Identify compounds using the Serch Lirry lgorithm Tsk 13. Identify compounds using the Serch Lirry lgorithm Step Detiled Instructions Comments 3 Close the dt file. Click File > Close Dt File. Click Close. If you wnt to sve these results, see Tsk 16. Sve results on pge 60. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 51

2 Find nd identify Tsk 14. Find compounds y MRM (MRM only) Tsk 14. Find compounds y MRM (MRM only) The Find Compounds y MRM lgorithm identifies compounds in MRM dt from Triple Qudrupole. The lgorithm serches for compounds using the MRM trnsitions. All of the compounds in the cquisition method re extrcted nd shown in the Compound List. Compounds re not eliminted sed on chromtogrm integrtion results. You cn only use the Find Compounds y MRM lgorithm on dt tht ws cquired using MRM trnsitions. The MRM lgorithm uses informtion tht is found in the dt file if the dt file is n MRM dt file. Tsk 14. Find compounds using MRM (MRM only) Step Detiled Instructions Comments 1 Open the TIC for the Pest - STD 200 MRM.d dt file. c If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the Pest - STD 200 MRM.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox nd click Open. You use the Generl Workflow when working with GC/QQQ dt. You cn use either the Generl Workflow or the GC/Q-TOF Compound Screening workflow when working with GC/Q-TOF dt. Figure 33 TIC chromtogrm from Pest - STD 200 MRM.d 2 Configure the user interfce to work with GC dt. Follow the instructions in Tsk 2. Configure User Interfce for GC/MS dt on pge 12. 52 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 14. Find compounds y MRM (MRM only) Tsk 14. Find compounds using MRM (MRM only) Step Detiled Instructions Comments 3 Find compounds using the MRM lgorithm. c d In the Method Explorer window, select Find Compounds > Find y MRM. Click the Group trnsitions y compound nme utton. Click the Integrtor t. Select the Agile integrtor. You cn choose the region of the chromtogrm from which you intend to find compounds. You cn extrct the complete result set for compound fter it is found y using the Compounds > Extrct Complete Result Set menu item when compound is highlighted. Figure 34 Integrtor t in the Find y MRM section of the Method Editor e Click to run the Find Compounds y MRM lgorithm on the dt file. f If necessry, click the View > Compound List commnd. g Click View > Compound Identifiction Results to open this window. The Qulittive Anlysis progrm finds 28 compounds under these conditions. 4 Exmine the compounds. See Figure 35 on pge 54. c d Select 2 in the Mximum numer of list pnes ox in the MS Spectrum Results toolr. Click the Hide Empty Columns icon in the Compound List window nd in the Compound Identifiction Results window. Click the first compound in the Dt Nvigtor window. When the Dt Nvigtor window is selected, use the rrow keys to switch compounds. The precursor ion is displyed in the Precursor (Acq Method) column, nd the product ion is displyed in the Product (Acq Method) column in the Compound Identifiction Results window. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 53

2 Find nd identify Tsk 14. Find compounds y MRM (MRM only) Tsk 14. Find compounds using MRM (MRM only) Step Detiled Instructions Comments Figure 35 Find y MRM results 5 Close the dt file. Click File > Close Dt File. Click Close. If you wnt to sve these results, see Tsk 16. Sve results on pge 60. 54 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 15. Generte formuls nd serch lirry for pek spectr Tsk 15. Generte formuls nd serch lirry for pek spectr In this tsk, you first integrte nd extrct pek spectr from GC/Q-TOF dt file. Then, you generte possile formuls for ech of the pek spectr. Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 1 Open the TIC for the MSD_mix_4stds_DB_spl200_03.d dt file. c If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DB_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox nd click Open. If the Lod result dt check ox is not ville, then no results hve een sved in the dt file. See Tsk 16. Sve results on pge 60 for instructions on how to sve results. 2 Integrte nd extrct pek spectr. Click the Chromtogrms > Integrte (MS) section in the Method Explorer window. Click the Pek Filters t. c Click the Pek height utton. d Mrk the Reltive height check ox. e Mrk the Limit (y height) to the lrgest check ox nd type 4. f Click Chromtogrms > Integrte nd Extrct Pek Spectr. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 55

2 Find nd identify Tsk 15. Generte formuls nd serch lirry for pek spectr Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 3 Generte formuls for ech pek spectr. View the Spectrum Identifiction Results List. Close the MS Spectrum Results window. Hint: To otin the sme results s in Figure 37, mke sure you hve selected Common orgnic molecules s the Isotope model. c d e f g h i In the Method Explorer window, click Identify Compounds > Generte Formuls. In the Method Editor window, click the Chrge Stte t, nd select Common orgnic molecules s the Isotope model. In the Dt Nvigtor window, highlight the first spectrum in the User Spectr. Click the Identify > Generte Formuls from Spectrum Peks commnd or the Generte Formuls from Spectrum Peks utton to run the lgorithm. Repet the previous two steps for every pek spectr. If necessry, click the Spectrum Identifiction Results icon,, or click the View > Spectrum Identifiction Results commnd. In the Spectrum Identifiction Results window, click the Automticlly Show Columns utton in the toolr. Click the Hide Empty Columns icon,,in the Spectrum Identifiction Results window. Close the Method Editor window. You cn see the predicted isotope undnce rtios on the spectrum plot when you zoom in t the pproprite m/z. See the online Help for more informtion. The Run icon in the Method Editor toolr sometimes llows you to choose n ction from set of possile ctions. For exmple, two different ctions re possile when you click the Run icon in this section. If you click the rrow, list of possile ctions is shown, nd you cn choose which ction to do. Choosing different ction from the list chnges the defult ction. If you simply click the Run utton, the defult ction is performed. You cn chnge the width of column y drgging the line tht seprtes djcent columns. You cn move column y drgging the column heder. You cn delete column y clicking Remove column in the shortcut menu in the tle. 56 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 15. Generte formuls nd serch lirry for pek spectr Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments Figure 36 Generte Formul results for peks 1 to 4 4 Do lirry serch for pek spectr 1 to 4. c d e In the Dt Nvigtor window, click User Spectr. In the Method Explorer window, click Identify Compounds > Serch Unit Mss Lirry. Verify tht vlid lirry is selected. Click Identify > Serch Lirry for Spectr in the min menu. Close the Method Editor window. The Method Editor is opened utomticlly when you click section in the Method Explorer. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 57

2 Find nd identify Tsk 15. Generte formuls nd serch lirry for pek spectr Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 5 Modify the columns tht re visile. c d Right-click the Spectrum Identifiction Results window nd click Add/Remove Columns. In the (Enhnced) Add/Remove Columns dilog ox, mrk the columns tht you wnt to disply. Cler the check oxes tht you do not wnt to disply. Click OK. Click the Hide Empty Columns icon,,in the Spectrum Identifiction Results window. If you use the Remove Column commnd nd remove column tht contins dt, the softwre utomticlly redisplys this column if the Automticlly Show Columns feture is on. The LiSerch lgorithm is weighted hevily in the Comine Identifiction Results section of the method. You cn mnully choose the est MFG result or chnge how identifiction results re comined. Figure 37 Results for Lirry Serch nd Generte Formuls for first pek spectr 58 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 15. Generte formuls nd serch lirry for pek spectr Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 6 (optionl) Close the dt file. You cn proceed to the next tsk to lern how to sve results. Click File > Close Dt File. Click Close. If you wnt to sve these results, see Tsk 16. Sve results on pge 60. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 59

2 Find nd identify Tsk 16. Sve results Tsk 16. Sve results In this tsk, you sve the results for the current dt file. Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 1 Sve the results for the current dt file nd close the dt file. Click File > Sve Results. Click File > Close Dt File. You cn only sve one set of results with dt file. If you lredy hve sved results with the current dt file, then these results re overwritten when you click File > Sve Results. 2 Open the dt file nd lod the results. c d Click File > Open. The Open Dt File dilog ox opens. Select dt file. For this exmple, select the dt file MSD_mix_4stds_DG_spl200_03.d. Mrk the Lod result dt check ox. Click the Open utton. The Lod result dt check ox is mrked. Figure 38 Open Dt File dilog ox 60 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 16. Sve results Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 3 Exmine the results. Click the Spectrum Identifiction Results window. Review the results. Figure 39 Results for Lirry Serch nd Generte Formuls for first pek spectr 4 Close the dt file. Click File > Close Dt File. Click Close. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 61

2 Find nd identify Tsk 16. Sve results Tsk 15. Generte formuls for pek spectr Step Detiled Instructions Comments 5 Open the dt file gin nd do not lod the results. c d Click File > Open. The Open Dt File dilog ox opens. Select dt file. For this exmple, select the dt file MSD_mix_4stds_DG_spl200_03.d. Cler the Lod result dt check ox. Click the Open utton. If you do not lod results, then y defult TIC is opened when you open dt file. If you mrk the Run File Open ctions from selected method check ox, then the File Open ctions re run, insted. See the online help for more informtion. Figure 40 Results for Lirry Serch nd Generte Formuls for first pek spectr 6 Close the dt file. Click File > Close Dt File. Click Close. 62 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Find nd identify 2 Tsk 16. Sve results Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 63

2 Find nd identify Tsk 16. Sve results 64 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Agilent MssHunter Worksttion Softwre Qulittive Anlysis Fmiliriztion Guide for GC/MS Exercise 3 Use workflows, export nd print Tsk 17. Set up nd run qulittive nlysis method using the generl workflow 66 Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow 71 Tsk 19. Export CEF file 74 Tsk 20. Print n nlysis report 75 Tsk 21. Print compound report 78 In these tsks, you lern to set up nd run qulittive nlysis method. Then you run the ctions within the utomted method when you open dt file. Two different workflows re used for these exmples. See Workflows on pge 89 for more informtion. The Generl workflow supports GC/QQQ, GC/Q-TOF nd LC/MS dt. The GC/Q-TOF Compound Screening workflow supports GC/Q-TOF dt. Ech exercise is presented in tle with three columns: Steps Use these generl instructions to proceed on your own to explore the progrm. Detiled Instructions Use these if you need help or prefer to use step-y-step lerning process. Comments Red these to lern tips nd dditionl informtion out ech step in the exercise. Agilent Technologies 65

3 Use workflows, export nd print Tsk 17. Set up nd run qulittive nlysis method using the generl workflow Tsk 17. Set up nd run qulittive nlysis method using the generl workflow When you first strt to use the Qulittive Anlysis progrm, the method defult.m is loded. You cn mke chnges to the opened method nd sve it, or open new method, mke chnges nd sve the method. You cnnot overwrite the method defult.m. You cn lso set up to run specific ctions in the method when you open dt file. When you open dt file, you cn lso lod the method tht ws used to crete the results tht re stored with the dt file. This method is utomticlly sved whenever you sve the results with the dt file. The Generl workflow cn e used with either GC/MS or LC/MS dt files. Tsk 17. Set up nd run qulittive nlysis method using the Generl workflow Steps Detiled Instructions Comments 1 Open the TIC for the Pest - STD 200 MRM.d dt file. c If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the Pest - STD 200 MRM.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox nd click Open. You use either the Generl Workflow or the GC/Q-TOF Compound Screening workflow when working with GC/MS dt. 2 Configure the user interfce to work with GC dt. Follow the instructions in Tsk 2. Configure User Interfce for GC/MS dt on pge 12. For this exmple, select the Generl workflow. 3 Set up the method to extrct TIC chromtogrm. Define TIC chromtogrm for MS dt. c d e In the Method Explorer window, select Chromtogrm > Define Chromtogrms. Delete the BPC chromtogrm. Select TIC s the Type. Mke sure the MS Level is MS/MS. Click Add. 66 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 17. Set up nd run qulittive nlysis method using the generl workflow Tsk 17. Set up nd run qulittive nlysis method using the Generl workflow Steps Detiled Instructions Comments 4 Edit the method to integrte the dt. Limit the integrtion to the four highest peks. In the Method Explorer window, click Chromtogrm > Integrte (MS/MS). Click the Pek Filters t. c In the Mximum numer of peks section, mrk the Limit (y height) to the lrgest check ox. d Type 4. Updting vlue in the Pek Filters t in the Chromtogrm > Integrte (MS) section lso updtes vlues in other sections of the Method Explorer. Blue tringles pper to show these other sections. You cn click the Sve Method icon to sve the current method. Figure 41 The Chromtogrm > Integrte (MS/MS) > Pek Filters t 5 Test the integrtion to mke sure tht only 4 integrted peks pper. 6 Sve the method to iii_gcexercise1, where iii re your initils. Click the Integrte Chromtogrm icon to integrte the dt file. From the top menu, click Method > Sve As. Type iii_gcexercise1. c Click the Sve utton. Note tht sving the method cuses ll the lue tringles indicting vlue chnges in the opened method to dispper. 7 Chnge the pek spectrum ckground to use the spectrum t the strt of pek. c In the Method Explorer window, click Spectrum > Extrct (MS/MS). Click Pek Spectrum Extrction (MS/MS). For the Pek spectrum ckground, select Spectrum t pek strt. If you mke ny dditionl chnges fter sving the method, then the lue tringles re dded. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 67

3 Use workflows, export nd print Tsk 17. Set up nd run qulittive nlysis method using the generl workflow Tsk 17. Set up nd run qulittive nlysis method using the Generl workflow Steps Detiled Instructions Comments You cn click the Sve Method icon to sve the current method. Figure 42 The Spectrum > Extrct (MS/MS) > Pek Spectrum Extrction (MS/MS) t 8 Test the MS spectrum extrction to mke sure ckground spectrum is sutrcted. Click the Extrct Pek Spectrum icon to run the ction on the selected pek in the dt file. 9 Sve the method. Sve the method in one of three wys: Click the Sve Method icon in the Method Editor. Right-click the Method Editor, nd click Sve Method. From the top menu click Method > Sve. The Sve Method icon is shown in Figure 42 on pge 68 10 Set up the method to utomte the ctions whose prmeters you just chnged when you open dt file. List the ctions to e performed when this or nother dt file is opened. Hint: Look under Generl in Method Explorer. In the Method Explorer window, select Generl > File Open Actions. Select Integrte nd Extrct Pek Spectr from the Aville ctions list. c Click the Add utton,, to move the selected ction to the Actions to e run list. You cn lso doule-click on the selected ction to move it to the other list. 68 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 17. Set up nd run qulittive nlysis method using the generl workflow Tsk 17. Set up nd run qulittive nlysis method using the Generl workflow Steps Detiled Instructions Comments 11 Test the File Open Actions. Click the Run File Open Actions Now icon to run the ctions on the dt file. The chromtogrms nd spectr re not overwritten. New chromtogrms nd spectr re dded. Two different ctions re prt of the Actions to e run list. The first ction is to extrct the defined chromtogrms. Then, tht chromtogrm is integrted nd peks re extrcted. Figure 43 The Generl > File Open Actions section in the Method Editor 12 Sve the method. Click the Sve Method icon in the Method Editor window, 13 Set up the method to utomte the ctions when the method is run during worklist. List the ctions to e performed when this or nother dt file is opened. Hint: Look under Worklist Automtion in the Method Explorer window In the Method Explorer window, select Worklist Automtion > Worklist Actions. Remove Generte Anlysis Report from the Actions to e run list. 14 Test the Worklist Actions. Click the Run Worklist Actions Now icon to run the ctions on the dt file. The chromtogrms nd spectr re not overwritten. New chromtogrms nd spectr re dded. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 69

3 Use workflows, export nd print Tsk 17. Set up nd run qulittive nlysis method using the generl workflow Tsk 17. Set up nd run qulittive nlysis method using the Generl workflow Steps Detiled Instructions Comments Two different lists of ctions re included in method. The first list of ctions (File Open Actions) cn e run when dt file is opened. The second list of ctions (Worklist Actions) is run when the method is run s prt of worklist. Figure 44 The Worklist Automtion > Worklist Actions section in the Method Editor 15 Sve the method nd close the dt file without sving results. Click the Sve Method icon in Method Editor, Click File > Close Dt File, nd click No when sked to sve results. 70 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow In this tsk you set up qulittive nlysis method tht contins list of nlysis ctions to run in specific order. These include extrcting nd integrting chromtogrms, extrcting spectr, serching lirry for pek spectr, generting formuls for spectr nd printing n nlysis report. Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Steps Detiled Instructions Comments 1 Open the TIC for the MSD_mix_4stds_DG_spl200_03.d dt file. c If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DG_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox nd click Open. 2 Configure the user interfce to work with GC dt. Follow the instructions in Tsk 2. Configure User Interfce for GC/MS dt on pge 12. For this exmple, select the GC/Q-TOF Compound Screening workflow. 3 Mke sure tht TIC is extrcted. Select Chromtogrm. Click the Define Chromtogrms t. c Mke sure tht TIC hs een selected s the Chromtogrm used to find mss spectr. d Click the Chnge utton. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 71

3 Use workflows, export nd print Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Steps Detiled Instructions Comments 4 Review prmeters for the Find y Chromtogrm Deconvolution lgorithm. c d e f Click the GC/Q-TOF Compound Screening > Find y Chromtogrm Deconvolution section in the Method Explorer window. Click the Mss Filter t. Set the Asolute height vlue to 13000. Click the Results t. Click the Highlight ll compounds utton. Review the results on ech t. Look t the sections for the GC/Q-TOF Compound Screening workflow. Note the six sections in this workflow. All of these sections re duplictes of sections tht re lredy prt of the method explorer. Note tht lue tringles pper in other sections of Method Explorer. These indicte tht the sme prmeter vlues hve een chnged elsewhere s well. 5 Review prmeters for the Identify y Lirry Serch lgorithm. c Click the GC/Q-TOF Compound Screening > Identify y lirry serch section in the Method Explorer window. Select lirry. Review the prmeters on ech t. Either the demo.l lirry or the NIST08.l (or other version of the NIST lirry) is instlled in the \MssHunter\Lirry folder. 6 Sve the method. Click the Sve Method icon in the Method Editor window, 7 Set up the method to utomte the ctions when dt file is opened. List the ctions to e performed when this or nother dt file is opened. Hint: Look under Generl in the Method Explorer window c d e f g In the Method Explorer window, select Generl > File Open Actions. Remove Generte Anlysis Report from the Actions to e run list. Remove Integrte nd Extrct Pek Spectr. Remove ny other ctions in the list. Add Extrct Defined Chromtogrms. Add Find Compounds y Chromtogrphic Deconvolution. Add Serch Spectrl Lirry for Compound. 8 Test the File Open Actions. Click the Run File Open Actions Now icon to run the ctions on the dt file. The chromtogrms nd spectr re not overwritten. New chromtogrms nd spectr re dded. 72 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow Steps Detiled Instructions Comments Figure 45 Results from running worklist ctions on the GC/Q-TOF dt 9 Sve the method to iii_gcexercise2, where iii re your initils. c From the menu, click Method > Sve As. Type iii_gcexercise2. Click Sve. If this method is run during Dt Acquisition worklist, then the Worklist Actions on this t re executed in the given order. 10 Close the dt file without sving results. Click File > Close Dt File. Click No when sked to sve results. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 73

3 Use workflows, export nd print Tsk 19. Export CEF file Tsk 19. Export CEF file You cn export CEF file contining compound informtion. This CEF file cn e imported into other progrms such s MssHunter Quntittive Anlysis nd Mss Profiler Professionl. You cn lso import compounds tht were exported in CEF file. Tsk 19. Export CEF file Steps Detiled Instructions Comments 1 Open the MSD_mix_4stds_DG_spl200_03.d dt file nd run the File Open ctions for the method iii_gcexercise2.m which ws creted in Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71. c d e If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DG_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox. Mrk the Run File Open ctions from selected method check ox. Click the Use current method utton nd click Open. If you finished Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71, then the current method is iii_gcexercise2.m. This method is set up to run the Find Compounds y Chromtogrm Deconvolution lgorithm nd then run the Serch Lirry lgorithm on ech compound. 2 Export CEF file. To interctively export the file, click File > Export > s CEF. Click the All results utton. c Select the loction of the export file. d Click OK. Figure 46 Export CEF Options dilog ox 74 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 20. Print n nlysis report Tsk 20. Print n nlysis report Whenever you wnt to print n nlysis report fter performing ny of the tsks in this exercise or the next one, use these instructions. An nlysis report cn contin the results from extrcting nd integrting chromtogrms, extrcting spectr, finding compounds, serching the dtse for pek spectr or generting formuls from pek spectr. Tsk 20. Print n nlysis report Steps Detiled Instructions Comments 1 If the MSD_mix_4stds_DG_spl200_03.d dt file is not loded, then open this dt file nd run the File Open ctions for the method iii_gcexercise2.m which ws creted in Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71. c d e If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DG_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox. Mrk the Run File Open ctions from selected method check ox. Click the Use current method utton nd click Open. If you finished Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71, then the current method is iii_gcexercise2.m. This method is set up to run the Find Compounds y Chromtogrm Deconvolution lgorithm nd then run the Serch Lirry lgorithm on ech compound. 2 Chnge the nlysis report selections in the method: Mrk the check oxes for the chromtogrms, spectr or tles you wnt to print. Cler the check oxes for the chromtogrms, spectr or tles you do not wnt to print. c In the Method Explorer window, click Reports > Anlysis Report. Mrk the check oxes for ny dditionl selections you wnt to print. Cler ny chromtogrm nd spectr choices you do not wnt to print. The Anlysis report only contins the informtion tht you mrk in this section. If some results re not ville, then those results re not included, even if those results re mrked in this section. For exmple, if you hve not integrted the chromtogrm, then the pek tle is not included. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 75

3 Use workflows, export nd print Tsk 20. Print n nlysis report Tsk 20. Print n nlysis report (continued) Steps Detiled Instructions Comments By defult, the Method Editor window is floting. It is visile s seprte window from the rest of the Qulittive Anlysis progrm. To nchor the window, right-click the title of the window nd click Floting. You cn lso doule-click the title r to nchor the window. Figure 47 Anlysis Report section in the Method Explorer nd Method Editor windows 3 Print the report. You cn interctively print the report in multiple wys: From the min menu, click File > Print > Anlysis Report. From the min toolr, click the Printer icon. Click the Print Anlysis Report icon, in the Method Editor toolr when the Anlysis Report section is selected. Right-click the Anlysis Report section in the Method Editor, nd click Print Anlysis Report. From the dt file shortcut menu in the Dt Nvigtor, click Anlysis Report. Click the Report contents. c Mrk the Print report check ox nd select printer. d Mrk the Print preview check ox. e Click the OK utton. f The Run icon in the Method Editor toolr sometimes llows you to choose n ction from set of possile ctions. For exmple, if you switch to the Reports > Common Reporting Options section of the Method Editor window, four different ctions re possile when you click the Run icon. If you click the rrow, list of possile ctions is shown, nd you cn choose which ction to do. Choosing different ction from the list chnges the defult ction. If you simply click the Run utton, the current defult ction is performed. 76 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 20. Print n nlysis report Tsk 20. Print n nlysis report (continued) Steps Detiled Instructions Comments Figure 48 Print Anlysis Report dilog ox g h Review the report. Click the Close Print Preview icon in the toolr. Figure 49 Print Preview window with Anlysis Report Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 77

3 Use workflows, export nd print Tsk 21. Print compound report Tsk 21. Print compound report Whenever you wnt to print compound report, use these instructions. Tsk 21. Print compound report Step Detiled Instructions Comments 1 If the MSD_mix_4stds_DG_spl200_03.d dt file is not loded, then open this dt file nd run the File Open ctions for the method iii_gcexercise2.m which ws creted in Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71. c d e If the progrm is not open, doule-click the Mss Hunter Qulittive Anlysis icon. Otherwise, click File > Open Dt File. Click the MSD_mix_4stds_DG_spl200_03.d dt file in the GC exmple dt file folder. Cler the Lod result dt check ox. Mrk the Run File Open ctions from selected method check ox. Click the Use current method utton nd click Open. If you finished Tsk 18. Set up nd run method using the GC/Q-TOF Compound Screening workflow on pge 71, then the current method is iii_gcexercise2.m. This method is set up to run the Find Compounds y Chromtogrm Deconvolution lgorithm nd then run the Serch Lirry lgorithm on ech compound. 2 Chnge some of the selections in the method for compound reports: Turn off viewing the MS spectr zoomed in on specil peks. Turn off the MS/MS options in the report. In Method Explorer, click Reports > Compound Report. Cler the Show MS spectrum check ox. c Cler the Show MS/MS spectrum check ox. d Cler the Show MS/MS pek tle check ox. These check oxes llow you to specify wht informtion to include in report if it is ville. If the informtion is not ville, tht section is utomticlly skipped. For exmple, MS/MS results re never included when the dt file only hs MS dt. 78 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Use workflows, export nd print 3 Tsk 21. Print compound report Tsk 21. Print compound report Step Detiled Instructions Comments Figure 50 Compound Report section in the Method Editor 3 (optionl) Choose different compound report templte. In the Method Explorer window, click Reports > Common Reporting Options. Select CompoundReport WithIdentifictionHits.xlsx s the Compound report templte. Severl different report templtes re included with the softwre. You cn customize report templte using Excel nd the Report Designer dd-in. You cn use Excel nd the Report Designer dd-in to customize ny of the templtes tht hve the extension XLTX. You cnnot customize the cquisition method report. Figure 51 Common Reporting Options section in the Method Editor Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 79

3 Use workflows, export nd print Tsk 21. Print compound report Tsk 21. Print compound report Step Detiled Instructions Comments 4 Print the report. Click File > Print > Compound Report or click the rrow in the Print Anlysis Report icon nd click Print Compound Report to print the compound report. Mrk the Print preview check ox. c Click OK. Exmine the report. d Click the Close Print Preview icon. In the Print Compound Report dilog ox, you cn select different printer, select to sve the report to PDF or Excel file, select whether to print ll results or only the highlighted results, nd whether or not to comine different dt files into one report. See the online Help or the Report Designer Trining DVD for dditionl informtion. Figure 52 Print Preview window with the Compound Report 5 Close the dt file without sving results. Click File > Close Dt File. Click No when sked if you wnt to sve the results. 80 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Agilent MssHunter Worksttion Softwre Qulittive Anlysis Fmiliriztion Guide for GC/MS Reference Work with windows 82 Work with result dt in Dt Nvigtor 84 Perform opertions on the chromtogrm 85 Perform opertions on n MS or MS/MS spectrum 86 Work with chromtogrphic visul dt 87 Work with spectrl visul dt 88 Workflows 89 Customize report templte 93 Agilent Technologies 81

4 Work with windows Work with windows When you first open the Qulittive Anlysis progrm, you see four windows in the defult lyout: Dt Nvigtor, Method Explorer, Chromtogrm Results nd MS Spectrum Results. You cn ring up sixteen other windows using the View menu: Method Editor - llows you to edit method prmeters seprted into different ts Spectrum Preview - llows you to quickly scn the spectr in dt file MS Spectrum Results - shows the MS nd MS/MS spectr Difference Results - shows the difference results fter lirry serch Deconvolution Results - shows the deconvoluted spectr UV Spectrum Results - shows the UV spectr - only ville for LC/MS dt Integrtion Pek List - shows the integrtion results in tle MS Spectrum Pek List 1 - shows the pek tle for the first spectrum selected MS Spectrum Pek List 2 - shows the pek tle for the second spectrum selected MS Actuls - shows cquisition informtion for the highlighted spectrum Compound List - shows the compounds tht re found using one of the Find Compounds lgorithms Compound Identifiction Results - shows the identifiction informtion for the selected compound Spectrum Identifiction Results - shows the identifiction informtion for the selected spectr MS/MS Formul Detils - shows tle contining possile formuls clculted for frgments seen in n MS/MS spectrum Structure Viewer - shows the structure ssocited with the current compound or spectr Smple Informtion - shows informtion out the highlighted dt file Sequence Editor - llows you to edit method sequence You cn lso disply three tool windows which re displyed when you strt using the ssocited tool: Formul Clcultor Mss Clcultor 82 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Work with windows 4 Reclirte Window Icons in the Min Toolr You open nd close the windows with these icons on the min toolr. Additionl icons re ville when the MssHunter BioConfirm softwre is instlled. Commnds in the View menu cn lso e used to open these windows. Dt Nvigtor Method Explorer Method Editor Chromtogrm Results UV Spectrum Results Spectrum Preview MS Spectrum Results Difference Results Deconvolution Results Integrtion Pek List Compound List MS Spectrum Pek List 1 MS Spectrum Pek List 2 MS Actuls Sequence Editor Compound Identifiction Results Spectrum Identifiction Results MS/MS Formul Detils Structure Viewer Smple Informtion Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 83

4 Work with result dt in Dt Nvigtor Work with result dt in Dt Nvigtor Dt Nvigtor window nd tools The Dt Nvigtor orgnizes ll the results of extrction nd spectrum selection either y dt file or y dt type. Linked Nvigtion Icon When ctivted (defult), highlighting chromtogrm in Dt Nvigtor lso highlights the corresponding spectr. The corresponding chromtogrm nd spectrum grphic results re lso highlighted. Linked Nvigtion only works if you hve used the Integrte nd Extrct Pek Spectr menu item from the Chromtogrms Menu or hve run ny of the Compounds lgorithms. Check Mrk Tools Single check mrk Mrks check oxes of ll highlighted dt. Dul check mrks, one gry Mrks check oxes of highlighted dt nd clers the other check oxes. Dul check mrks Mrks ll check oxes. Chromtogrms nd spectr re displyed when their check oxes re mrked. 84 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Perform opertions on the chromtogrm 4 Perform opertions on the chromtogrm You cn perform the following opertions on the whole chromtogrm or on selected region of the chromtogrm y using the menu items: Action Chnge pek lels in chromtogrm Extrct chromtogrm Extrct defined chromtogrms Integrte the chromtogrm Integrte nd extrct pek spectr Smooth the chromtogrm Clculte Signl-to-Noise Sutrct ny chromtogrm Find compounds from uto MS/MS dt Find compounds from trgeted MS/MS dt Find compounds for MS(1) dt Find compounds for MRM dt Find compounds y chromtogrm deconvolution Find compounds tht mtch specific formuls Menu Item Configurtion > Chromtogrm Disply Options Chromtogrms > Extrct Chromtogrms Chromtogrms > Extrct Defined Chromtogrms Chromtogrms > Integrte Chromtogrm Chromtogrms > Integrte nd Extrct Pek Spectr Chromtogrms > Smooth Chromtogrm Chromtogrms > Clculte Signl-to-Noise Chromtogrms > Sutrct Any Chromtogrm Find > Find Compounds y Auto MS/MS Find > Find Compounds y Trgeted MS/MS Find > Find Compounds y Moleculr Feture Find > Find Compounds y MRM Find > Find Compounds y Chromtogrm Deconvolution Find > Find Compounds y Formul Select rnge opertions from shortcut menu When you hve selected chromtogrphic rnge, you cn lso extrct spectrum nd extrct spectrum to ckground, in ddition to the opertions mentioned ove nd others not mentioned. 1 To ccess these opertions, click the Rnge Select tool ( ) in the Chromtogrm Results toolr. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 85

4 Perform opertions on n MS or MS/MS spectrum 2 Click t the point where you wnt to strt the rnge, drg the cursor over rnge, nd relese the mouse utton. 3 Right-click nywhere in the chromtogrm, nd click the opertion from the shortcut menu. Sve results to the dt file(s) Click the Sve icon ( ), or click File > Sve Results. When you exit the progrm, it lso sks if you wnt to sve the results to the dt file, unless you hve turned off this feture (you turn off this feture in the Messge Box Options dilog ox) Perform opertions on n MS or MS/MS spectrum You cn perform the following opertions on n MS or MS/MS spectrum or on selected region of n MS or MS/MS spectrum y using the menu items: Action View the m/z, undnce, chrge stte nd other informtion out peks in spectrum Chnge the spectrl pek lels Sutrct the ckground spectrum Sutrct ny spectrum Add two spectr together Serch dtse for entries tht mtch specific msses in spectrum Generte formuls for the msses in the selected rnge in spectrum Serch Lirry Menu Item View > MS Spectrum Pek List 1 Configurtion > MS nd MS/MS Spectr Disply Options Spectr > Sutrct Bckground Spectrum Spectr > Sutrct Any Spectrum (nd then click nother spectrum) Spectr > Add Any Spectrum (nd then click nother spectrum) Spectr > Serch Dtse for Spectrum Peks Spectr > Generte Formuls from Spectrum Peks (when rnge is selected in the MS spectrum) Identify > Serch Lirry for Spectr or Spectr > Serch Lirry for Spectr 86 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Work with chromtogrphic visul dt 4 Work with chromtogrphic visul dt Chromtogrm Results Window Chromtogrm Results Tools Zoom Tools in order Select Tools in order To cler tool selection, click nother tool or icon. Autoscle X-xis nd Y-xis Autoscle X-xis Autoscle Y-xis Unzoom Autoscle Y-xis during Zoom Linked Y-xis mode Rnge Select When On, you cn drw rnge for chromtogrm, for which you cn perform ctions. Pek Select When On, you cn select spectrum of n integrted pek t pex. Mnul Integrtion When On, you cn integrte interctively. Wlk Chromtogrm When On, you cn see individul spectr s you click ech point or use the left nd right rrows on the keyord. Annottion When On, you cn dd imge nd text nnottions to the chromtogrms. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 87

4 Work with spectrl visul dt Work with spectrl visul dt MS Spectrum Results Window MS Spectrum Results Tools Zoom Tools in order Select Tools in order Autoscle X-xis nd Y-xis Autoscle X-xis Autoscle Y-xis Unzoom Autoscle Y-xis during Zoom Linked Y-xis mode To cler tool selection, click nother tool or icon. Rnge Select When On, you cn drw rnge for chromtogrm, for which you cn perform ctions Annottion When On, you cn dd imge nd text nnottions to the chromtogrms Clipers When On, you cn dd Delt Mss cliper to the selected spectrum. In the Deconvolution Results window, you cn lso dd n Amino Acid cliper or Modifictions cliper. See the online Help for more informtion. 88 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Workflows 4 Workflows Workflows help you to customize the user interfce for your ppliction. Ech workflow lods different method tht hs prmeters tht re pproprite for tht workflow. Also, ech workflow lods different lyout; these lyouts include customizing the columns shown in ech tle. Lstly, four of the lyouts lso dd specil method editor section which contins copies of the sections in the method editor tht re importnt for tht workflow. Grouping the fetures tht re used in specific workflow together mkes it esier for you to customize your method. Severl different workflows re ville in the Qulittive Anlysis progrm. They re: Generl BioConfirm - These workflows re only ville if the BioConfirm softwre is instlled nd mrked in the User Interfce Configurtion dilog ox. BioConfirm hs severl possile workflows, depending on the type of nlysis tht you wnt to do. Chromtogrm Pek Survey Formul Confirmtion nd Smple Purity MS Trget Compound Screening GC/Q-TOF Compound Screening If you re working with GC/MS dt, you cn select the Generl workflow or the GC/Q-TOF Compound Screening workflow. If you re working with LC/MS dt, you cn select ny of the workflows except for GC Q-TOF Compound Screening. Specific Method Ech workflow lods specific defult method with more pproprite settings for tht workflow. For exmple, if you switch to one of the BioConfirm workflows, the Trget dt type for the Find Compounds y Moleculr Feture lgorithm is set to Lrge molecules (proteins, oligos). This setting is pproprite for the BioConfirm workflow ut not, y defult, for the other workflows. Specific Lyout In ddition, ech workflow lods specific lyout. A lyout consists of the following: Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 89

4 Workflows Ech window s position nd size Which windows re ted Which windows re floting Which ted window is on top Which windows re visile y defult Whether the sttus r is visile For ech plot window (the Chromtogrm Results window, the Spectrum Preview window, the MS Spectrum Results window, the Deconvolution window nd the UV Results window), the following re sved: Whether or not the grphics re overlid Whether or not the Autoscle Y-Axis during Zoom mode is on Whether or not the Linked Y-Axis mode is on For ech tle window, the following re sved Which columns re visile The order of the columns The width of ech column Any filter tht hs een dded to the tle (only ville for the Compound List tle, the Compound Identifiction Results tle, nd the Spectrum Identifiction Results window). Specific section in the Method Explorer nd Method Editor Using the Method Editor with the Generl workflow, you cn chnge lmost ll of the prmeters in the Method. Ech of the four other workflows chnges the sections ville in the Method Explorer. Ech new section contins only the Method Editor ts nd sections tht re useful in tht workflow. Chnging prmeter in the workflow section lso chnges the prmeter in the corresponding section in the generl Method Editor sections. Two ts re not repeted in the generl Method Editor sections. The Chromtogrm Pek Survey Workflow > Spectrum Pek Identifiction section nd the Chromtogrm Pek Survey Workflow > Chromtogrm Extrction > Chromtogrms t re only included in the Chromtogrm Pek Survey workflow. These sections only ffect the Chromtogrm Pek 90 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Workflows 4 Survey lgorithm. This lgorithm is only used in this workflow, nd in the Chromtogrm Pek Survey without Report ction nd in the Chromtogrm Pek Survey with Anlysis Report ction. Workflow methods nd lyouts Additionl defult methods nd lyouts re provided for ech workflow. Workflow Method Lyout Method Editor Section Generl defult.m Defult.xml None BioConfirm Intct Protein BioConfirm IntctProtein- Defult.m BioConfirm- IntctProtein- MximumEntropy- Defult.xml BioConfirm Workflow BioConfirm High Mss Intct Protein BioConfirm IntctProtein HighMss Defult.m BioConfirm IntctProtein LMFE.xml BioConfirm Workflow BioConfirm Smll Oligonucleotides BioConfirmOligo nucleotidesmll.m BioConfirmOligonucleotide.xml BioConfirm Workflow BioConfirm Lrge Oligonucleotides BioConfirmOligo nucleotidelrge- Defult.m BioConfirmOligonucleotide.xml BioConfirm Workflow BioConfirm Protein Digest BioConfirmProtein Digest-Defult.m BioConfirm ProteinDigest.xml BioConfirm Workflow BioConfirm Synthetic Peptide BioConfirmSynthetic Peptide-Defult.m BioConfirm SyntheticPeptide.xml BioConfirm Workflow Chromtogrm Pek Survey ChromPekSurvey- Defult.m Defult.xml Chromtogrm Pek Survey Workflow Formul Confirmtion nd Smple Purity SmplePurity- Defult.m SmplePurity- Defult.xml Formul Confirmtion nd Smple Purity Workflow Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 91

4 Workflows Workflow Method Lyout Method Editor Section MS Trget Compound Screening GC Q-TOF Compound Screening Screening-Defult.m Screening-Defult.xml MS Trget Compound Screening Workflow GC_Q-TOF.m QTOFDt.xml GC/Q-TOF Compound Screening 92 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide

Customize report templte 4 Customize report templte Plese refer to either the online Help for the MssHunter Report Designer Add-in, the Report Designer Fmiliriztion Guide or the Reporting Trining DVD for detiled informtion on how to modify report templte. The following steps give you quick look t wht it mens to customize templte. 1 Go to the folder tht contins the report templtes. By defult, this folder is \MssHunter\Report Templtes\Qul\B.05.00\en-US\Letter. You cn select different folder in the Method Explorer in the Generl > Common Reporting Options > Templtes t. 2 Mke copy of the templte which you intend to modify. Right-click the copy nd click Properties. If necessry, cler the Red-only check ox. Then, right-click the copy nd click Open from the shortcut menu. Opening the templte this wy lets Excel know tht this file is templte file. When the templte is open, you cn modify heders nd footers nd dd, remove or move prmeter columns. Refer to the online Help for more informtion. All Qulittive Anlysis templtes re mrked Red-only. You chnge this property efore you edit templte. Mny templtes re instlled with the Qulittive Anlysis progrm. Refer to the Qulittive Anlysis online Help for more informtion out the content of ech report templte. Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide for GC/MS 93

4 Customize report templte 3 Mke the chnges you wnt to mke. For more informtion on how to modify templte, see either the online Help for the MssHunter Report Designer dd-in, or the Agilent MssHunter Reporting - Trining DVD. 4 To sve the new templte, either click Sve or click Sve As > Other Formts from the Microsoft Office utton. 5 Type n identifying nme, nd click Sve. 94 Agilent MssHunter Worksttion Softwre - Qulittive Anlysis Fmiliriztion Guide