Agilent Mass Hunter Software

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1 Agilent Mss Hunter Softwre Quick Strt Guide Use this guide to get strted with the Mss Hunter softwre. Wht is Mss Hunter Softwre? Mss Hunter is n integrl prt of Agilent TOF softwre (version A.02.00). Mss Hunter opertes on chromtogrphic nd electrophoretic mss spectrl dt to extrct informtion to reduce dt complexity, eliminte potentil interferences, nd generte list of moleculr fetures. Working with the extrcted informtion A feture is discrete moleculr entity defined y the comintion of retention time nd mss. You cn use the feture informtion from Mss Hunter to perform mny different tsks. Here re few exmples: Compre the originl (rw dt) totl ion chromtogrm (TIC) with the processed TIC Compre the originl nd processed mss spectr t specific retention time (RT), or verged over n RT rnge, on the TIC Show extrcted ion chromtogrms sed on mss spectrl rnge. View the species clusters (isotopic, dimers, dducts) for ech feture For complete list of tsks, see the Mss Hunter online help. Agilent Technologies

2 Getting strted with the Mss Hunter softwre Strt the Mss Hunter softwre This section tells you how to strt the Mss Hunter softwre. Either do this: Doule-click the Agilent TOF Softwre folder icon on the desktop, or Select Strt > Progrms > Agilent > TOF Softwre from the desktop. In the Agilent TOF Softwre folder, doule-click the Mss Hunter icon. Or do this: Select Strt > Progrms > Agilent > TOF Softwre > Mss Hunter from the desktop. The system displys the Mss Hunter min window. Lern how to ccess Mss Hunter functions You cn use the toolr or the menus to perform mny of the Mss Hunter tsks: HINT To ccess other functions, doule-click or Ctrl-click plot or tle row numer. You my use the middle mouse utton click for Ctrl-click in the Mss Hunter softwre 2 Agilent Mss Hunter Softwre Quick Strt Guide

3 Lern how to use Mss Hunter Try these exercises to fmilirize yourself with the Mss Hunter ppliction. Try the Steps on the left in the exercises on the next pges without the Detiled Instructions. If you need more help, follow the detiled instructions. If you wnt to do this: Extrct feture informtion Extrct feture informtion for single file Extrct feture informtion for tch Reprocess file with different prmeters Disply specific feture informtion or export nd sve informtion Show species clusters, mss spectr nd extrcted ion chromtogrms (EIC) for fetures Show possile feture compositions Export nd sve feture informtion Work with chromtogrms, mss spectr nd contour plots Show mss spectr from chromtogrms nd show nd hide other plots Show EICs from mss spectr Lern to use contour plots Refer to this section or exercise: Exercises: Extrcting feture informtion on pge 4 Exercise 1 Extrct feture informtion for single file on pge 4 Exercise 2 Extrct feture informtion for tch on pge 9 Exercise 3 Reprocess files with different prmeters on pge 11 Exercises: Reviewing nd sving feture informtion on pge 14 Exercise 4 Show species clusters, EIC nd mss spectr for fetures on pge 14. Exercise 5 Show possile feture compositions on pge 17 Exercise 6 Export nd sve feture informtion on pge 19 Exercises: Working with plots on pge 22 Exercise 7 Working with processed chromtogrms (TICs or EICs) on pge 22 Exercise 8 Working with mss spectr on pge 24 Exercise 9 Working with contour plots on pge 25 Agilent Mss Hunter Softwre Quick Strt Guide 3

4 Exercises: Extrcting feture informtion Exercise 1 Extrct feture informtion for single file This exercise guides you through the process to extrct feture informtion from TOF.wiff file. CAUTION To process Agilent TOF dt files (.wiff files) with the Mss Hunter softwre, the.wiff files must e locl to the softwre. Tht is, the files must reside on the computer where the Mss Hunter softwre is running. Also, the files must not e red-only. Use Windows Explorer to check nd chnge the file ttriutes. Steps Detiled Instructions Comments 1 Open UrineNeg 1027_9_1A.wiff. Copy the exmple Mss Hunter files tht come with the TOF softwre to folder tht only you will use. c d Select File > Open File. Go to your folder tht contins the Mss Hunter exmple TOF dt files. Select UrineNeg 1027_9_1A.wiff. Click Open. The dt file ppers in the Rw Dt Window. (See Figure 1.) This exmple file contins single smple time segment nd scn dt. When you open dt file tht contins multiple dt sets, the Select Dt Set dilog ox (Figure 2) ppers. You must then select one comintion of smple, time segment nd scn segment to extrct efore the Rw Dt Window ppers. Figure 1 Rw Dt Window 4 Agilent Mss Hunter Softwre Quick Strt Guide

5 Steps Detiled Instructions Comments Figure 2 Select dt set dilog ox Agilent Mss Hunter Softwre Quick Strt Guide 5

Steps Detiled Instructions Comments 2 View the mss spectr nd pek informtion of the rw dt t retention time of 8.9 min. Doule-click the TIC t 8.9 minutes.

6 Steps Detiled Instructions Comments 2 View the mss spectr nd pek informtion of the rw dt t retention time of 8.9 min. Doule-click the TIC t 8.9 minutes. Two mss spectr for tht RT pper elow the TIC, nd the pek informtion for the mss spectrum ppers in the Rw Dt Pek Viewer on the left. One mss spectrum shows the seline, nd the other shows the threshold level, which cn e chnged y the user (see Exercise 3 Reprocess files with different prmeters on pge 11). 6 Agilent Mss Hunter Softwre Quick Strt Guide

Relese the mouse utton. Repet the zoom until you see the lue line. 4 Sve the TIC imge to file. Right-click the TIC.

7 Steps Detiled Instructions Comments 3 View the threshold level for the mss spectrum etween 400 nd 600 m/z. c In the lower spectr viewer, hold the mouse utton down nd drw rectngle t the seline etween 400 nd 600 m/z. Relese the mouse utton. Repet the zoom until you see the lue line. 4 Sve the TIC imge to file. Right-click the TIC. Select Imge > Sve to File > Bitmp. c Go to the folder into which you wnt to plce the file, nd enter the file nme. d Click Sve. Agilent Mss Hunter Softwre Quick Strt Guide 7

wiff file with the sme set of extrction prmeters (see Exercise 3 Reprocess files with different prmeters on pge 11) s the ones stored in the *.mhd file, the progrm simply lods the result from the *.

8 Steps Detiled Instructions Comments 5 Process the file. An.mhd file is creted upon processing. This file contins he extrction result. Although you cn open this file directly, you should open the originl.wiff file so tht you ccess more informtion. Note: if you ttempt to process the *.wiff file with the sme set of extrction prmeters (see Exercise 3 Reprocess files with different prmeters on pge 11) s the ones stored in the *.mhd file, the progrm simply lods the result from the *.mhd file. Select Process > Run, or click the Process utton on the toolr. The processed totl ion chromtogrm ppers under the originl TIC in the Processed Dt Window (Figure 3), nd the Feture Summry Tle ppers in the Fetures Viewer. An Excel file is utomticlly creted contining ttriutes for ech feture. The Excel file tkes the nme of the.wiff file processed. In this cse, the file is nmed UrineNeg1027_9_1A.xls. (Figure 4). Figure 3 Processed Dt Window Figure 4 Excel spredsheet with feture informtion utomticlly sved fter processing 8 Agilent Mss Hunter Softwre Quick Strt Guide

Exercise 2 Extrct feture informtion for tch This exercise shows you how to utomticlly extrct feture informtion for tch of TOF dt files for downstrem use or lter review.

9 Exercise 2 Extrct feture informtion for tch This exercise shows you how to utomticlly extrct feture informtion for tch of TOF dt files for downstrem use or lter review. CAUTION To process Agilent TOF dt files (.wiff files) with the Mss Hunter softwre, the.wiff files must e locl to the softwre. Tht is, the files must reside on the computer where the Mss Hunter softwre is running. Also, the files must not e red-only. Use Windows Explorer to check nd chnge the file ttriutes. Steps Detiled Instructions Comments 1 Crete tch of files to extrct. Use the following files: All three smple 9.wiff files: UrineNeg1027_0_3A.wiff, UrineNeg1027_9_2A.wiff, nd UrineNeg1027_9_1A.wiff. The first file in the smple 10 folder: UrineNeg1027_10_2A.wiff Select Btch > Crete. Or, click the Crete Btch utton in the toolr. Hold the Shift key s you select ll three files in the smple 9 folder, nd click Open. The Btch Process Window (Figure 5) ppers with the.wiff files from smple 9 listed. c Click the Crete Btch utton in the toolr gin. d Select the first file in the smple 10 e folder. Click Open. The Btch Process Window now contins ll four files. If ny of the.wiff files contins more thn one dt set, the Btch Dt Set Options dilog ox ppers. You then select if you wnt to use ll the dt sets in ll the files or one spectr set per file. If you click One spectr set per file, the Select Dt Set dilog ox ppers. For more detils out using these dilog oxes, see the Mss Hunter online help. Figure 5 Btch Process Window Agilent Mss Hunter Softwre Quick Strt Guide 9

10 Steps Detiled Instructions Comments 2 Process the files. Select Process > Execute Btch, or click the Process utton in the toolr. Notice the Progress r on the left. When the runs re complete for ll dt files, you see messge sying tht the tch run is complete. To see the fetures, groups nd mss spectr for ech of the processed.mhd files in the tch, you must open ech individully nd work with it in the Processed Dt Window. 10 Agilent Mss Hunter Softwre Quick Strt Guide

Exercise 3 Reprocess files with different prmeters You cn reprocess originl.wiff files or lredy processed.mhd files with new extrction prmeters.

11 Exercise 3 Reprocess files with different prmeters You cn reprocess originl.wiff files or lredy processed.mhd files with new extrction prmeters. Steps Detiled Instructions Comments 1 Open the file UrineNeg 1027_9_1A.wiff. 2 Chnge the extrction prmeters: RT rnge of 6 to 12 minutes m/z rnge of 300 to x 1000 mss spectrl peks Select File > Open File. Select UrineNeg 1027_9_1A.wiff, nd click Open. Select Settings > Extrction Prmeters, or click the Extrction Prmeters utton in the toolr. Agilent Mss Hunter Softwre Quick Strt Guide 11

Steps Detiled Instructions Comments c d e To set the RT rnge, enter 6 s the Min RT nd 12 s the Mx RT. To set the m/z rnge, enter 300 s the Min M/Z nd 800 s the Mx M/Z.

12 Steps Detiled Instructions Comments c d e To set the RT rnge, enter 6 s the Min RT nd 12 s the Mx RT. To set the m/z rnge, enter 300 s the Min M/Z nd 800 s the Mx M/Z. For the Mx spectrl peks to use, enter 250. Click OK. 3 Reprocess the file. Becuse the open.wiff file ws previously processed nd produced n.mhd file, the system displys the Reprocessing Options dilog ox. Mke sure to reprocess the file nd not lod the old results. Select Process > Run, or click the Process utton in the toolr. Click Reprocess in the Reprocessing Options dilog ox. This dilog ox ppers only when you try to process newly opened *.wiff file which hs een processed previously. If you try to reprocess file whose feture informtion is displyed now, the softwre ssumes tht is your intention nd will not show the dilog. 12 Agilent Mss Hunter Softwre Quick Strt Guide

13 Steps Detiled Instructions Comments 4 Review the extrction prmeters used for the current result. Select View > Prmeter Tle. Close the tle fter review. You my wnt to occsionlly review the prmeters used to disply the currently displyed results. Agilent Mss Hunter Softwre Quick Strt Guide 13

Exercises: Reviewing nd sving feture informtion Exercise 4 Show species clusters, EIC nd mss spectr for fetures The Feture Summry Tle presents list of fetures nd their ttriutes.

14 Exercises: Reviewing nd sving feture informtion Exercise 4 Show species clusters, EIC nd mss spectr for fetures The Feture Summry Tle presents list of fetures nd their ttriutes. When coelution grouping is enled (defult), the list presents group fetures tht coelute t lmost equivlent retention times. This exercise shows you how to ring up the Feture Detils Tle, which lists the fetures nd their species clusters for the coeluting group. When coelution grouping is disled, the two tles list only individul fetures. Steps Detiled Instructions Comments 1 Disply the species clusters for the fetures tht coelute together in group. Disply group #2 in the.wiff file. Doule-click row 25 of the Feture Summry Tle. Doule-clicking the row heder of ny feture of the group rings up the Feture Detils Tle for the group. The Feture Detils Tle contins the species clusters for the fetures in the group. The Plot Viewer displys the mss spectr for the group of fetures, s well s the EIC for the group. 14 Agilent Mss Hunter Softwre Quick Strt Guide

Doule-click the row numer 1 in the Feture Detils Tle.

15 Steps Detiled Instructions Comments 2 Show the feture mss spectr nd EIC for the first feture in the group. Doule-click the row numer 1 in the Feture Detils Tle. The mss spectr nd EICs pper for tht feture. Agilent Mss Hunter Softwre Quick Strt Guide 15

Steps Detiled Instructions Comments 3 Show ion mss spectr nd EICs for the M+H ion of the second feture in the group. Doule-click the row #9 in the Feture Detils tle.

16 Steps Detiled Instructions Comments 3 Show ion mss spectr nd EICs for the M+H ion of the second feture in the group. Doule-click the row #9 in the Feture Detils tle. The Plot Viewer displys the mss spectrum nd EIC for the originl dt, nd mss spectrum nd EIC for the processed ion specified in row 9. 4 Show feture mss spectr for feture when coelution grouping is disled. Select Settings > Disle Coelution Grouping. Click the Process icon to ring up the Feture Summry Tle with listing of fetures nd no groups. c Doule-click the row #2. You now see the Feture Detils Tle with species cluster informtion for only tht feture. The mss spectr for the selected feture pper in the Plot Viewer, nd the species clusters for tht feture only pper in the Feture Detils Tle. 5 Re-enle Coelution Grouping. Select Settings > Enle Coelution Grouping. Click the Process icon. 16 Agilent Mss Hunter Softwre Quick Strt Guide

Exercise 5 Show possile feture compositions The Mss Hunter softwre clcultes the possile compositions for ny feture you select either from the Feture Summry Tle or the Feture Detils Tle.

Steps Detiled Instructions Comments 1 Disply the possile compositions for feture t row 15. In the Feture Summry tle, right-click row #15 t the row heder.

17 Exercise 5 Show possile feture compositions The Mss Hunter softwre clcultes the possile compositions for ny feture you select either from the Feture Summry Tle or the Feture Detils Tle. This exercise shows you how to disply these compositions nd set up the rules for clculting the composition. Steps Detiled Instructions Comments 1 Disply the possile compositions for feture t row 15. In the Feture Summry tle, right-click row #15 t the row heder. When you click Composition, the Possile Compositions dilog ox ppers with the possile compositions listed. If the MW is greter thn 800 mu, wrning messge ppers to let you know tht the clcultion my tke while nd to sk you if you wnt to continue. Click Composition. Agilent Mss Hunter Softwre Quick Strt Guide 17

Steps Detiled Instructions Comments 2 Add isotope N15 to the list of elements used in the clcultion. In the Possile Compositions dilog ox, click Chemistry.

In the Composition Info dilog ox, click Add/Remove. c d In the Select Elements dilog ox, right-click N nd select isotope 15N. Click OK.

18 Steps Detiled Instructions Comments 2 Add isotope N15 to the list of elements used in the clcultion. In the Possile Compositions dilog ox, click Chemistry. After you follow these instructions, Mss Hunter dds the N15 isotope to the element list. The isotope ppers t the ottom of the Periodic Tle with mrked checkox. In the Composition Info dilog ox, click Add/Remove. c d In the Select Elements dilog ox, right-click N nd select isotope 15N. Click OK. 3 Set up the clcultion so tht the softwre uses no fewer thn zero nd no more thn 10 N15. Enter the Min numer of toms for N15 of 0 nd Mx numer of 10. Click OK. When you click OK, the softwre utomticlly reclcultes the possile compositions. 18 Agilent Mss Hunter Softwre Quick Strt Guide

19 Exercise 6 Export nd sve feture informtion You cn export the informtion in ech Mss Hunter tle to n Excel file: Feture Summry Tle Feture Detils Tle Possile Compositions Tle Prmeter View You cn lso sve moleculr ion pek informtion for ll the fetures. Steps Detiled Instructions Comments 1 Export the Feture Composition tle to Microsoft Excel file. If you re lredy in the Possile Compositions dilog ox fter Exercise 5, skip to step. View the Excel file. c d e f g Right-click ny feture in the Feture Summry Tle, nd click Composition. Click Export. Specify destintion folder. Specify file nme. Click OK. Close the Possile Compositions dilog ox. Go to the folder contining the Excel file, nd open the file. If you re in the Mss Hunter min window, open the file UrineNeg1027_9_1A_1_1_1.mhd. Then follow the instructions in this step. 2 Export the Feture Summry tle to Microsoft Excel file. View the Excel file. c d e At the top of the Feture Summry Tle, click Export. Specify destintion folder. Specify file nme. Click OK. Go to the folder contining the Excel file, nd open the file. See Figure 6, Feture Summry Tle in Excel, on pge Export the Feture Detils tle. View the Excel file. f g h i j At the top of the Feture Detils Tle, click Export. Specify destintion folder. Specify file nme. Click OK. Go to the folder contining the Excel file, nd open the file. See Figure 7, Feture Detils Tle in Excel, on pge 21. If the Feture Detils Tle is not present, doule-click the row numer of the group or feture of interest in the Feture Summry Tle. Agilent Mss Hunter Softwre Quick Strt Guide 19

Steps Detiled Instructions Comments 4 Sve nd view the moleculr ion informtion. c d Select File > Sve Feture Info. Specify destintion folder. Click OK.

20 Steps Detiled Instructions Comments 4 Sve nd view the moleculr ion informtion. c d Select File > Sve Feture Info. Specify destintion folder. Click OK. Go to the folder contining the Excel file, nd open the file. See Figure 8, Feture Info Tle in Excel, on pge 21. Figure 6 Feture Summry Tle in Excel 20 Agilent Mss Hunter Softwre Quick Strt Guide

21 Figure 7 Feture Detils Tle in Excel Figure 8 Feture Info Tle in Excel Agilent Mss Hunter Softwre Quick Strt Guide 21

22 Exercises: Working with plots Exercise 7 Working with processed chromtogrms (TICs or EICs) You cn perform the chromtogrm opertions on totl ion chromtogrms (TICs) nd extrcted ion chromtogrms (EICs) nd on the originl nd processed chromtogrms, either together or seprtely. Steps Detiled Instructions Comments 1 Do the following: Zoom in on the chromtogrms etween 8 to 10 minutes to include the entire pek round 9 minutes. Zoom out the chromtogrm. c Hold the mouse utton down s you drw rectngle round the specified time window. Relese the mouse utton. Click the Full Zoom Out utton. When the zoom function is locked (defult), the zoom works on oth chromtogrms simultneously. If you click the Lock utton to unlock the zoom function, you cn zoom in or out of ech chromtogrm seprtely. 2 View the mss spectr (originl nd processed) t round RT 9 minutes. Doule-click the RT t round 9 minues in the chromtogrm. The system displys the mss spectrum t RT 9 min. for oth the originl nd processed chromtogrms. 3 View the verge mss spectr over the rnge of RT 8 to 10 minutes. c CTRL-click the left mouse utton (or click the middle mouse utton) to plce line on the plot to set the low end of the rnge over which the verge is clculted. CTRL-click the left mouse utton gin to plce line on the plot to set the high end of the rnge. Right-click the imge, nd select Ave MS Rnge. See Figure 9, Chromtogrphic rnge context menu, on pge 23. The verge mss spectr clculted over the selected rnge ppers elow the chromtogrm plots for the originl chromtogrm nd the processed chromtogrm. 4 Hide the TIC. Right-click the imge, nd select Hide EIC from the context menu (see Figure 9). When n EIC is superimposed on TIC, you cn hide the TIC. 5 Re-show the TIC. Right-click the imge, nd select Show EIC from the context menu. 22 Agilent Mss Hunter Softwre Quick Strt Guide

23 Figure 9 Chromtogrphic rnge context menu Agilent Mss Hunter Softwre Quick Strt Guide 23

Exercise 8 Working with mss spectr Steps Detiled Instructions Comments 1 Show n extrcted ion chromtogrm t out 500 m/z (highest pek) 1 Doule-click the highest pek in the mss spectrum.

24 Exercise 8 Working with mss spectr Steps Detiled Instructions Comments 1 Show n extrcted ion chromtogrm t out 500 m/z (highest pek) 1 Doule-click the highest pek in the mss spectrum. The Plot Viewer displys the EIC for this RT in oth the originl nd processed chromtogrm windows. 2 Show n extrcted ion chromtogrm for the m/z rnge of 500 to 550 m/z (pproximte). c CTRL-click the left mouse utton (or click the middle mouse utton) to plce line on the mss spectrum to set the low end of the rnge over which the chromtogrm is extrcted. CTRL-click the left mouse utton gin to plce line on the mss spectrum to set the high end of the rnge. Right-click the imge, nd select Show EIC from the context menu. The EICs pper superimposed on the TICs. 24 Agilent Mss Hunter Softwre Quick Strt Guide

25 Exercise 9 Working with contour plots The contour plot is two-dimensionl representtion of 3D dt, with m/z s the x-xis, RT s the y-xis nd intensity s the z-xis (the drkness or lightness of the imge on the plot). Two plots re shown, one for the originl dt nd the other, for the processed dt. Steps Detiled Instructions Comments 1 Show the contour plots. Right-click ny one of the chromtogrms, nd select Show Contour Plot. See Figure 9, Chromtogrphic rnge context menu, on pge 23. The contour plots pper for the originl nd processed chromtogrms. 2 Zoom into nd out of the contour plot. c Hold down the mouse utton nd drw rectngle round the re of interest. Relese the mouse utton. To zoom out, click the Zoom Out utton next to the coordintes text field. 3 Find the position of m/z= 500 nd RT=9. c CTRL-click the left mouse utton (or click the middle mouse utton). Two perpendiculr lue lines (cross-hir cursor) pper in the plot. With the mouse utton held down, move the cross-hir cursor to the point specified in step 3. Doule-click the plot to remove the cross-hir cursor. You cn see the coordintes of the position in the ox to the left nd elow the left contour plot. (Figure 10) 4 Hide the contour plot. Right-click the plot, nd select Hide Counter Plot. Agilent Mss Hunter Softwre Quick Strt Guide 25

26 Figure 10 Contour Plots with cross-hir cursor 26 Agilent Mss Hunter Softwre Quick Strt Guide

28 In this guide This Quick Strt Guide includes n overview of the Mss Hunter softwre, quick reference informtion to get strted using the softwre, nd set of tutorils to lern how to use the softwre. Agilent Technologies, Inc Printed in USA First edition, Septemer 2005 *G * G Agilent Technologies

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