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Xcalibur 2.1–2.3 Creating and Searching Libraries User Guide

1. 84 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Searching a Library Using Library Browser 7 Right click an entry in the Hit List pane to copy it to the first position in the Spec List pane see Figure 71 Figure 71 Library Browser default window showing file copying from Hit List to Spec List panes Name steroids 4451 69 RT 0 59 0 75 AV 19 NL 6 6 Formuka MW N A CAS N A NISTH N A ID 11 DB Text Fil Other DBs None Comment F e Full ms2 363 30 40 00 1 50 00 37 5 10 largest peaks 309 999 327969 2467507 281 449 291 249 407 297389 251 380 269314 263 150 190 23 270 310 350 Text File steroids 4 51 6F RT 0 59 0 75 AV 19 NL 6 62 ristde mo ms2test 747 totalspectra 10 1000900 800 700 600 500 400 300 200 100 0 hydro 150 170 310 330 350 370 hydro roi 0 590 e hrocortsoneMms2 hydro i hydro Name hydrocortisone sS2 hydro Formula hydro MW N A CAS N A NIST N A ID 1 DB ms2test hydro Other DBs None stero Comment F c Full ms2 363 30 40 00 1 50 00 375 00 Prog 10 largest peaks Endrin 309 999 327962 267 505 291 449 281 44 deox 249 401 297391 251 380 269315 263312 deox 0 Synonyms 150 190 230 ro synonyms ms2test hydrocortisone 52 Plot Text of Hit 8 To print the search results click Print in the tool bar See Library Sample
2. ard Detector ICIS Peak Integration r Limit peaks 3 a i mMin Type MENE Fesk Detect ICIS H Smoothing points fis Delay nit E 00 Baseline window jo me Select by aea Filter 7 Area noise factor E Select by height Trace TIC 7 x l z Peak noise factor fio TPR Num to select fic Aass m z 50 00 2000 00 I Constrain peak width m Rel peak height threshold Peak height Zi 5 0 T Enable Select top peaks Range min fo 0 999 0 Teina fector fi 0 of highest peak fic Eh Cancel Save As Default Advanced Help Reports retention time window Programs C AXcalibartexamplestdatatsteroids14 02128196 12 15 58 PM RT 0 00 3 78 SM 15G E teroids14 860 RT 0 67 P NL 1 9985 a 100 RT 0 67 NL T c Full m22 363 30 40 00 150 00 375 00 267 28 309 12 i 100 327 16 30 g Fo ao 5 2 60 203 13 lt i 5 25117 E v 40 g 20 E 20 a300 0o26 043 I i 0 0 os 1 0 15 2 0 25 3 0 35 150 200 250 300 350 Time min miz Ready NUM NOT SAVED 4 3 Select a detector type on the Identification page Thermo Scientific Creating and Searching Libraries User Guide 65 4 Searching Libraries Setting Up to Search Libraries Automatically 4 Select a peak detect algorithm in the Peak Detect list to specify how the data system finds and processes chromatogram peaks ICIS This algorithm h
3. In the Mass Spectral Peak Constraints table click the first available Type list Click the arrow and select from the four available conditions Normal Loss Rank or Maxmass In the same row select the m z box In a Normal Rank or Maxmass type constraint use this box to type the m z value of the mass spectral peak to be constrained In a Loss type constraint use this box to type the value of a neutral loss In the same row select the From box In a Normal Loss or Maxmass type constraint use this box to type the minimum abundance of the constrained mass spectral peak In a Rank type constraint use this box to type the lowest position of the ion in an intensity ordered list of spectral peaks In the same row select the To box In a Normal Loss or Maxmass type constraint use this box to type the maximum abundance of the constrained mass spectral peak In a Rank type constraint use this box to type the highest position of the ion in an intensity ordered list of spectral peaks Repeat steps 3 6 on the next available row to add further peaks to the Mass Spectral Peak Constraints table If you specify the same number in both fields the designated ion must have that rank in the retrieved spectrum Note If you switch between Absolute and Relative modes the Xcalibur data system prompts you with a warning dialog box before clearing all rows in the grid Creating and Searching Libraries User Guide Thermo Sc
4. M Select to constrain the library search to compounds containing specific elements using the Individual Element or Elements in Compound methods You can use the two types of elemental constraints together but make sure there are no contradictions For example you might put C 0 in the Individual Element group and then list C in the Elements in Compound box When a contradiction occurs a warning dialog box opens Elements In Compound Elements Specify a list of elements that must be present in search results To enter an element list click the box and type the IUPAC approved abbreviation for each element Separate each element in the list of up to 30 characters by a comma All Specify that the Xcalibur data system should return search results containing all and only the listed elements For example C H O would return HCHO but not CO2 CH4 or CH2C12 Compare these results with the Some option Some Specify that the Xcalibur data system return search results that contain at least one of the specified elements and no elements that are unlisted For example C H O would return CO2 CH4 HCHO but not CH2C12 Compare these results with the All option Clear Thermo Scientific Delete the text in the Elements in Compounds box Creating and Searching Libraries User Guide 117 C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page para
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6. Include replicate entries from the NIST library in the target library Include replicate entries in the target library Otherwise leave the box unchecked Note This check box is only active if you are converting from a NIST library to another format Replicate library browse Specify the location of a replicate library To change the replicate library click Browse and select the folder for the replicate library on your computer or network If you specify a replicate library the Xcalibur data system adds replicate entries into the appropriate replicate library If you select the library type NIST the Xcalibur data system displays the path to the NIST replicate library folder in the Library box You specify this location when you install NIST software Button Convert Thermo Scientific Start the library conversion you have specified using the Convert Libraries page The data system opens the Library Conversion Status dialog box and displays the Conversion Status progress bar and the Conversion Status box The Status bar displays messages such as the following Processed 100 of the entries continuing on The Conversion Status box displays sequential chronological top to bottom messages such as the following e Started the conversion on SEP 3 1999 at 10 01 please wait e Finished the conversion on SEP 3 1999 at 10 02 e Converted 570 entries Creating and Searching Libraries User Guide 109 C Library Referen
7. c Full 3 ms2 363 30 40 00 ae I 804 150 00 375 00 MS steroids14 704 604 505 Relative Abundance steroidsl4 Start s 1 End s 323 S RT 0 00 3 78 a Start F F F F Thermo Scientific Time 0 00 End Time 3 303 30040 315 30040 331 30040 363 30040 ull ms2 ull ms2 ull ms2 ull ms2 oo oo oo oo ji 77 100 100 100 150 8 NL 2 34E6 TIC MS steroids14 1005 00 310 J 00 320 00 350 00 375 Relative Abundance 0 27 0 47 0 5 f Time min To define the second range release the mouse button When you release the mouse button the data system subtracts an average of the selected scans and redraws the Spectrum view The Spectrum view header shows the number of subtracted scans For example SB 12 0 52 0 56 0 92 0 99 indicates the following e Qual Browser has applied background subtraction to the spectrum by using a 12 scan average e Retention time ranges used in the subtraction are 0 52 to 0 56 min and 0 92 to 0 99 min Creating and Searching Libraries User Guide 21 2 Adding a Spectrum to a Library Exporting Spectra from the Xcalibur Data System Exporting Spectra from the Xcalibur Data System To create a library entry for a custom library export a spectrum from the Spectrum view of Qual Browser to the Library Browser To export spectra from the data system to the Library Browser use one of these methods
8. 0 00 Samp Wt 0 00 Inj Yol uL 20 00 Comments Inst Method C pitcon trial2 steroidMSMSis Proc Method Cs pitcon trial2 Data Path C pitcon trial2 steroidMSMSis NL 1 9256 TCF c Full ms2 MS steroids 14 3 6 88 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids M 5 RT 0 67 P NL 2 10E5 T Full ms2 363 30 40 00 150 00 375 00 0 8 i 2 4 a 2 10 20 wo w0 wo 200 220 240 260 280 300 320 340 360 myz Difference Spectra R owdota Library entry Q QO 5 ue 5 244 263 285 288 208 301 327345 lt E 5 0 0 200 220 240 260 280 300 320 340 372 m z Library Spectrum of Most Probable Hit SI 775 RSI 775 MSTEST Entry 1 CAS NA Hycrocortisonems2 100 ap 3y g g9 at 267 wam A 71 297 gt ta me wT Wi ji a g I7 7 2 315 0 3g 2 363 37 150 20 250 300 350 mz Tabie of Results RT Scan Probability Name SI RSI CAS 0 67 59 98 76 HydrocortisoneMS2 775 775 NA 0 67 59 0 98 ProgesteroneMS2 374 551 NA 0 67 59 0 20 Deox ycorticosteroneMS2 325 461 NA 0 67 59 0 00 MethyltestosteroneMS 2 275 424 NA Thermo Scientific Creating and Searching Libraries User Guide 89 A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 4 121 RT 140 P NL 5 2064 T cFul ms2 33130 40 00 100 00 350 00 100 BO
9. 150 220 290 360 167 46 265 T steroids14 51 75 RT 0 59 0 Thermo Scientific Creating and Searching Libraries User Guide 99 ee i AMDIS Compound Identification This topic appendix describes using AMDIS to automate compound identification The Automated Mass Spectral Deconvolution amp Identification System AMDIS is a computer program developed to reduce the effort involved in identifying compounds by GC MS while maintaining the level of reliability associated with traditional analysis AMDIS extracts spectra for individual components from GC MS data and uses these spectra to identify compounds by matching these spectra with spectra in a reference library Contents e AMDIS Overview e Automated Compound Identification Using AMDIS AMDIS Overview AMDIS uses an extension of the published model peak approach as the basis for the calculations used to extract pure component spectra from complex chromatograms The model peak approach uses selected ion chromatograms as models for component shape Based on the shape individual mass spectral peak abundance profiles are extracted to produce a purified spectrum AMDIS was developed at NIST with the support of the Defense Threat Reduction Agency DOD NIST reports that the model peak method was successfully used for target compound identification in a large scale EPA study The first version of AMDIS was released September 1996 and AMDIS has been distributed at no additio
10. see Figure 36 Figure 36 Libraries page of the Library Search Options dialog box Library Search Options Search Libraries Automation Limits Constraints Available Libs Included Libs xi tle 174948 Spectra in 2 Libraries 174948 Spectra in 2 Libraries Cancel Help To access this page click the Libraries tab of the Library Search Options dialog box The Libraries page is divided into two panes Available Libs Lists libraries defined within the Library Browser Included Libs Lists the libraries used by the Library Browser in searches in the search order Thermo Scientific Creating and Searching Libraries User Guide 51 4 Searching Libraries Customizing a Search To change the search order of included libraries Use the up and down arrows To include a library in the search 1 Select the library name in the Available Libs list 2 Click Add To exclude a library from a search 1 Select the library name in the Included Libs list 2 Click the Delete button large red X Limiting a Library Search To examine or modify search constraints click the Constraints tab of the Library Search Options dialog box Constraints are divided into six categories e Molecular Weight e Name Fragment e Elements Value e Elements Present e Peaks e Other Databases For details about limiting a library search see Library Search Constraints Page Library View on page 115 52 Creating and Searchin
11. 1 Set parameters and save your settings by clicking OK To save your settings as a default for future searches click Save as Default Creating and Searching Libraries User Guide 57 4 Searching Libraries Limiting a Library Search Applying a Molecular Weight Constraint To limit the library search to compounds with a specific molecular weight or molecular weight range 1 Select the Enable check box in the Molecular Weight area see Figure 42 Figure 42 Molecular weight area Molecular weight MV Enable TTTeeeeeeeeneeee Range fi 999999 2 To type a molecular weight or molecular weight range use the Range box To specify a range use the format low mass high mass The valid range is 1 to 999999 All search results must satisfy the specified molecular weight range Note This constraint is not available if you have already clicked the Search with MW option on the Library Search Options page Applying the Other Databases Constraint To limit the library search to entries in the NIST library that are also featured in other databases 1 Select the Enable check box in the Other Databases area see Figure 43 NIST library entries contain references to other commercial databases if they contain information about the compound Figure 43 Other databases area Other databases MV Enable Fine i l TSCA EINECS RTECS IR T EPA USP M Hopoc Clear All 58 Creating and Searching Libraries User Gu
12. 199 P NL 2 2864 T c Ful ms2 331 30 40 00 100 00 350 00 w0 i 604 109 1 Z 69 1 i ga MET Bo 20 23 2 Bel Q wo 2o uo 60 Difference Spectra Relative Abundance 277 2 225 3 2953 253 1 239 1 38 2 267 3 B70 28 2851 348 4 180 200 220 240 260 280 300 320 340 360 rtz R owdota Library entry po 120 40 KO W0 200 220 240 260 280 300 320 345 m z Library Spectrum of Most Probable Hit SI 739 RSI 744 MSZIEST Entry 2 CAS NA DeoxycorticosteroneMS2 100 7S 8 H 107 253 27 s 60 313 27 F m 7 cies 213 21 os 5 145 157 R x 3 x os 183 25 Q 317 331 u9 100 150 20 250 30 35C m z Table of Results RT Scan Probability Name SI RSI CAS 1 39 117 98 63 DeoxycorticosteroneMS2 739 744 NA 1 39 117 0 98 MethyltestosteroneMS2 412 563 NA 1 39 117 0 30 ProgesteroneMS2 387 429 NA 1 39 117 0 00 HydrocortisoneMS2 350 395 NA Thermo Scientific Creating and Searching Libraries User Guide 95 A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 15 164 RT 199 P NL 6 8664 T Ful ms2 303 30 40 00 100 00 3 10 00 0 267 2 2852 Relative Abundance gt gt o aei 2393 25 1 Difference Spectra R owdota Library entry 20 Relative Abundance Laiti 2O 40 60 BO 200 220 240 m z Library Spectrum of Most Probable Hit SI 790 RSI 795 MS2TEST Entry 3 CAS NA Methyltestosteronems2 267 Relat
13. 60 AQ Relative Abundance 45 3 90 573 VIl 0 100 Difference Spectra Rawdota Library entry v c Le cen Cc 2 lt 2 5 ia ae 200 220 240 2 amp 0 280 300 m z Library Spectrum of Most Probable Hit SI 768 RSI 748 MSZTEST Entry 2 CAS NA DeoxycorticosteroneMs2 25 Relative Abundance Ol fazi gag 300 3x Table of Results RT Scan Probability Name 1 40 121 97 83 DeoxycorticosteroneMS2 1 40 121 0 97 HydrocortisoneMS2 1 40 121 0 67 ProgesteroneMS 2 1 40 121 0 00 MethyltestosteroneMS2 90 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 4 167 RT 198 P NL 8 2464 T c Ful rr62 303 30 40 00 00 00 310 00 267 2 Relative Abundance fo 2414 2591 100 120 40 0 180 200 220 240 260 280 300 320 340 360 Difference Spectra R awda Library entry 24 259 266 275 298 Relative Abundance vo ro vo w60 80 200 220 240 260 280 30 m z Library Spectrum of Most Probable Hit 51720 RSI 79t MS2TEST Enty 3 CASH NA MethyltestosteroneMs2 267 Relative Abundance Table of Results RT Scan Probability Name Sl RSI CAS 1 98 167 98 58 MethyltestosteroneMS2 790 791 NA 1 98 167 0 98 Deox ycorticosteroneMS 2 313 315 NA 1 98 167 0 33 HydrocortisoneMS2 289 292 NA 1 98 167 0 00 ProgesteroneMS2 264 347 NA
14. 60 70 mainib Acetamide N 4 ethoxypheny Name Acetamide N 4 ethoxyphenyl Formuka C10H1 3NO2 MWN 179 CASH 62 44 2 NIST 107172 ID 2176 DB mainib Other DBs Fine TSC A RTECS EPA USP HODOC NIH EINECS Contributor N W Davies Centr Sci Lab Uriv Tasmaria Hobart Australa 10 largest peaks 108999 109860 179 4 137424 43340 81110 80109 44103 53 85 180 76 Synonyms p Acetopheretidide 2 p Ethox yac etariide 3 Acetopheretidin 4 Acetopheretidine 5 Acetopheretin 6 Feridina 7 Ferina 8 Kalmin 9 N Acety p phenetidine 10 Pertonal 11 Phenacetine 12 Phenazetin 13 Phenedina 14 Pheridin p Allylphenyl methyl ether Palmita Palmitic acid Palmitic acid a monoglyc eride Palmitic acid butylester Palmitic acid esters Palmitic acid isopropylester Palmitic acid methylester Palmitin 1 mono Paknyl p a Dic hlorotoluene With the a to z only no prefix option selected the Browser accepts only alphabetic characters and ignores common prefixes for example cis trans dl di and tri numbers and Greek characters In this mode typing butene finds 1 butene and cis 2 butene Thermo Scientific Creating and Searching Libraries User Guide 9 1 Overview of Library Browser Library Browser Windows Compare Window The Compare window is used for the comparison of spectra only it has no searching capabilities It supports comparison of any set of spectra and unlike the Library search window
15. 999 327964 267505 281 450 2914 249 402 297392 251380 2469316 2632 150 190 230 270 310 350 Synonyms v mainib repib ms2test 174950 totalspectra Text File steroids 4451 72 RT 0 59 0 78 AV 22 SB 29 C gt 100 Plot Text of Search Spectrum Plot of Search Spectrum Plot Text of Spec List sterol Structures Spec List 10 1 fo 1000 900 800 700 400 500 400 300 200 1 1004 RMatch Prob yy ae 999 9560 hydra E 150 170 190 210 230 250 270 20 30 330 350 370 ms 453 654 095 hydro Pf asteroids 4451 72 RT 0 59 0 78 AV Differerce ha hydrocortisone 52 R 445 463 0 71 Endrin Difference A_Headto Tail Side by Side j _Subtraction_ 999 999R 95 6P R 444 444 0 71 Endrin i M 443 529 0 65 Germ roe alae R 432 451 0 7 Endrin MW N A CASH N A NIST N A ID 2 DB ms2 est M 424 524 0 31 Germ Other DBs Nore M 417 44l 024 Andr Comment F c Full ms2 363 30 40 00 1 50 00 375 00 M 415 485 0 71 Endrin 10 largest peaks M 4l4 426 0 21 7 Hyd 309999 327964 267 505 281 450 291 448 M 397 397 011 Butan 249 402 297392 251380 2469316 263311 M 389 390 0 08 Erdos Synonyms M 388 397 008 12 13 ro synonyms la AA nor or akaki fur 150 190 230 ms2test hydrocortisonen 2 ii B Plot Text of Hit A Plot of Hit Compare Librarian Ident Ident l l l 32 Creating and Searching Libraries User Guide Thermo Scientific 3 Manag
16. Colchicine STDEMO Folic Acid STDEMO l7aMethyltestost STDEMO Hydrochlorothiaz STDEMO Reserpine STDEMO HO Distannoxane he STDEMO Squalane STDEMO oH oH Ergotarrine Tartr STDEMO o Relatie Abunctance y A y Ae a a A A Nig A Diethylstilbestrol STDEMO Suilfica vazala NUSTOFAAC steroids 4451 75 RT Raw data Library entry 0 59 0 82 AV 25 NL 5 1 3E4 F c Fullms2 363 30 40 00 150 00 375 00 73 z 157161 173 181 1 4 70 2T 1 1980 RSI981 MS2TEST 57 161 173 181 205 215 225 249 270275 292 305 327 345355 Entry 1 CAS NA Hydrocortisone S2 Relttive Abundarce Relative Abundance NUM The interactive cells of the Library Search Results view show the following library search results displayed clockwise from the upper left quadrant e Hits list search results e Molecular structure including formula molecular weight name and library index number Difference spectrum Raw Data minus Library Entry Peaks above the X axis are relatively more intense in the spectrum than in the library entry Peaks below the X axis are relatively more intense in the library entry than in the sample spectrum Thermo Scientific Creating and Searching Libraries User Guide 79 4 Searching Libraries Searching a Library Using Library Browser e Comparison of the sample spectrum and the library entry 7 To print the library search report choose File gt Print Preview The Print dial
17. If you select the library type NIST the Xcalibur data system displays the path to the NIST library folder in the Library box You specified this location when you installed NIST Library Browse Target View the file folder to store the converted library file To change the folder click Browse and select the target folder on your computer or network Title Target Type in a title for the ICIS GCQ ITS 40 library or for the Mass Lab library that you create during the conversion You can add a title to the new library using any format Note This box in the Target library details area only becomes active when you select an ICIS GCQ ITS 40 or MassLab library 108 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Manager Dialog Box Table 3 Convert Libraries page parameters Sheet 2 of 2 Parameter Description Add the library to the Add the converted library to the NIST software for use with the data system NIST software for use with xcalibur Options Target library action Create Replace Create a new library in the target directory or to replace an existing library You can also append add the new converted entries to a previously created target library Target library action Append Append adds the new converted entries to a previously created target library You can also create a new library in the target directory or to replace an existing library
18. Name hydrocortisoneM 2 Formula MW N A CASH N A NISTH N A ID 1 DB ms2test Other DBs None Comment F c Full ms2 363 30 40 00 1 50 00 375 00 10 bargest peaks 309 999 327962 2467505 291 449 281 448 249 401 297391 251380 269315 263312 Synonyms ne synonyms 10 Close the windows and return to the Xcalibur Home Page a Choose File gt Exit to close Library Browser and return to Qual Browser b Choose File gt Exit again to close the Qual Browser window and return to the Xcalibur Home Page 42 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Managing the NIST Libraries Managing the NIST Libraries To add delete or move a library from the NIST libraries list use the Manage Libraries page in the Xcalibur Library Manager dialog box This section shows you how to complete the following tasks e Adding a Library e Deleting a Library e Copying a Library To open the Xcalibur Library Manager 1 If the Xcalibur Home Page is not already open on the computer choose Start gt All Programs gt Thermo Xcalibur gt Xcalibur Verify that the home page is open in the Roadmap view 2 To open the Library Manager Dialog Box choose Tools gt Library Manager The Library Manager opens on the Manage Libraries page by default see Figure 31 Figure 31 Manage Libraries page Xcalibur Library Manager Manage libraries Convert libraries NI
19. Number 52875 CAS Number 272504 Peaks 69 Library mainlib Add to Library jeplace Add to List 10 Structure MAINLIB Exit Help Table 10 Spectrum Information dialog box parameters Sheet 1 of 2 Parameters Action Name Type a name for the spectrum Formula Type the chemical formula for example C12H8C160 Other Names Type synonyms for the compound Comments Type any comments about the spectrum Mol Weight NIST MS Search assigns a molecular weight based on the formula If no formula is available type the molecular weight ID Number View the ID number assigned to the library entry 122 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Results Window Table 10 Spectrum Information dialog box parameters Sheet 2 of 2 Parameters Action CAS Number View the CAS number for the compound You need not enter this information Peaks View the number of peaks in the mass list Buttons Add to Library Add the edited spectrum and structure to an existing or new library Replace Replace the spectrum in the library from which it came Add to List Add the edited spectrum to the Spec List Attach Struct Obtain a structure from other libraries Clipboard Struct Attach a structure from the clipboard if present To edit the mass list use the Peaks Info area Library Search Results Window Hit List Ther
20. Options Dialog Box socsie d cosets aeenwsed axed wie 111 Search Parameters Page enfants att Sin bee Ske aaa RAL ares ee 112 Libraries Page orio cae E ea igs Baie ow at e TAN a niet 113 Automation Pager ens eiaei ra AE e E ay alain ay tee 114 Limits Pages nenea eia a Ron wanes a a pee Sis karan 114 Library Search Constraints Page Library View 00000005 115 Spectrum Information Dialog Box 02 0 4 0 cca torent eles eek oe le 122 Library Search Results Window ti th 4 oust aoe ca gd Hom bnew bake dlaigantas 123 dek sirian canna s sad anata a tansa taal L RERE a dank aK 125 Creating and Searching Libraries User Guide v ee i Preface The Thermo Xcalibur mass spectrometry data system includes all the software needed to create search and edit libraries This guide describes e How to create and edit custom libraries for MS MS MS or MSn spectra e How to manage multiple libraries e How to search multiple libraries To provide us with comments about this document please click the link below Thank you in advance for your help SURVEY Related Documentation Thermo Fisher Scientific provides these documents for the Xcalibur data system Xcalibur Getting Started Guide for Quantitative Analysis e Xcalibur Data Acquisition and Processing User Guide e Xcalibur Quantitative Analysis User Guide Xcalibur Qualitative Analysis User Guide e Xcalibur Creating and Searching Libraries User Guide e XReport User Guide e H
21. The full spectrum or expanded views of a selected m z range e The compound structure if available The Text panes display the following e Compound Information name formula molecular weight CAS number NIST number ID number and search library e The ten largest peaks in the mass spectrum e Synonyms or alternate names used in the library Thermo Scientific Creating and Searching Libraries User Guide 7 1 Overview of Library Browser Library Browser Windows Other Search Window The Other Search window of the Library Browser see Figure 3 can carry out searches based on the following e Formula ID number e Molecular weight e Any peaks e CAS Registry number e Sequential method e NIST library number Launch these searches by selecting the appropriate option from the Search Type list in the top left corner of the window or use the appropriate command from the Search menu For more information about modifying searches see Searching Libraries on page 49 Figure 3 E MW 225 7 spectra GA Molecular Weight z i Mw 225 v t ju ib 8 Creating and Searching Libraries User Guide Other Search window History list NH2 On Sa 192 208 224 O 51 65 778593 107 119 136 148 40 60 80 100 120 140 mainib Phenethylamine 3 4 5 trimethox y a methy Name Phenethylamine 3 4 5 trimethox y a methyt Formuka C12H19 NO3 MW 225 CAS 1082 88 8 NIST 248106 ID 101 DB mainib Other
22. alcohols or specify that only certain elements can be present in the compound Limit a library search to increase processing efficiency For example you might want to exclude certain high intensity ions that appear in many compounds or that are present in the spectrum background You can target a search to a particular range of molecular weights or to compounds containing certain elements This view is available both in the Library Browser and the Qual Browser Table 9 Library Search Constraints Page parameters Sheet 1 of 7 Parameter Molecular Weight Description M Limit the library search to compounds with a specific molecular weight or molecular weight range by selecting the Molecular Weight Enable check box Range Type a molecular weight or molecular weight range in the box for example 200 250 During a search the Xcalibur data system only compares processed spectra with reference data derived from compounds with a molecular weight within the specified range Name Fragment M Limit the library search to compounds with a specific name or name fragment by selecting the Name Fragment Enable check box Name Thermo Scientific Type a text string up to 39 characters to represent a fragment of a compound name for example cyclo During the library search the Xcalibur data system filters search results and only returns those containing the specified text in their names The entry is not case sensitiv
23. comparison Use Constraints Libraries Page Set additional constraints on the search Use the Libraries page to specify the libraries used and the search order for them It is possible to keep different lists of active libraries for each of the search modes Table 6 Libraries page parameters Parameter Library Lists Description Available Libraries List the libraries that are currently excluded from searching during processing The Xcalibur data system regenerates this list when you open the dialog box Included Libraries List the libraries that are currently included in searches during processing The order of the libraries defines the order in which they are searched by the data system Buttons Remove Transfer a library from the Selected Libraries list to the Available Libraries list Up Move a library in the Selected Libraries list up one position earlier in the search order Down Move a library in the Selected Libraries list down one position later in the search order Thermo Scientific Creating and Searching Libraries User Guide 113 C Library Reference Library Search Options Dialog Box Automation Page Use the Automation page to specify values for an automated library search Table 7 Automation page parameters Parameter Number of hits to print Description Set the number of spectra to be printed per page The default value of 2 prints the unknown and the top two matches on a
24. creating entries in 15 16 43 46 deleting from NIST Libraries list 44 searching from Library Browser 80 from Qual Browser 77 Library Browser about 3 contents 83 exporting spectra to 22 figure 23 Creating and Searching Libraries User Guide 125 Index M library search constraining 52 Library Browser 6 options in Library Browser 51 processing method search list 63 selecting libraries 51 Library Search Constraints page element constraints 60 elements in compound 61 figure 57 mass spectral peak constraints 61 molecular weight 58 name fragment 59 Library Search Options dialog box 28 Library Search Options page append to user library 29 figure 54 options 55 library search processing 63 Library Search Property dialog box See Library Search Options dialog box Library Search Results window 123 Library Search window 5 limiting a library search 52 57 Mass spectral peak constraints 61 Match factor threshold 29 molecular weight constraining a library search 58 0 Name Fragment constraint 59 Name search window 9 Names window 9 National Institute of Standards and Technology 1 3 NIH NCI Inventory File database 59 NIST Browser 3 NIST MS Search 3 NIST EPA Gas Phase IR database 59 opening a raw data file in Qual Browser 15 Other Search window 8 overview of Library Browser 1 126 Creating and Searching Libraries User Guide P Plot pane 7 printing reports in Library Brow
25. gives the file an extension of msd and truncates the filename to the first eight characters of the original filename e Creates an index file containing details about the exported spectrum 80 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Searching a Library Using Library Browser When Library Browser opens the Xcalibur data system automatically does the following e Picks up the index file e Locates the exported msd spectrum files and lists them in the Spec List pane 4 To define search parameters in Library Browser choose Tools gt Library Search Options to display the Library Search Property dialog box see Figure 67 Figure 67 Library Search Property dialog box Search Property Thermo Scientific Creating and Searching Libraries User Guide 81 4 Searching Libraries Searching a Library Using Library Browser 5 Click the Libraries tab to display the list of available and included libraries see Figure 68 Use this dialog box to specify which libraries to search and the search order Figure 68 Libraries dialog box Library Search Options Search Libraries Automation Limits Constraints _ Libs Included Libs X 6 mainii mine mainlib 2379 Spectra in 2 Libraries 2378 Spectra in 1 Library e To add a library to the search list select its name in the Available Libs list and click Add e To exclude a library from the search list select its name
26. in few databases This option is Compounds effective only when you have selected one or more of the NIST databases such as MAINLIB It has no effect on spectra in user libraries or other commercial libraries Each reference spectrum in a NIST library contains a record of other commercial databases containing information about the compound A compound is considered rare if it is present in a limited number of these databases If you select the Penalize Rare Compounds option search result compounds present in few or no other databases other than the NIST libraries will have their match factors reduced the maximum penalty is 50 out of 1000 This in effect leads to a relative increase in the match factors of common compounds placing them higher in the hit list than exotic isomers with near identical spectra Pre search Default Off Turn off the pre search option MW Restrict the search to library entries with a particular molecular weight Type the molecular weight in the associated box 112 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Table 5 Search Parameters page parameters Sheet 2 of 2 Parameter Other Options Description Automation Indicate whether automatic library searching is enabled AutoReport Print reports of the results of library searching with user spectrum Apply Limits Set limits of m z and peak abundance for spectral
27. it or other libraries Set up libraries to search them automatically or search them manually from Qual Browser or Library Browser Contents e Customizing a Search e Setting Library Search Option Parameters e Submitting a Spectrum to a Library Search e Limiting a Library Search e Selecting Libraries to Search e Setting Up to Search Libraries Automatically e Processing Raw Files and Printing Reports e Initiating a Library Search from Qual Browser e Searching a Library Using Library Browser Thermo Scientific Creating and Searching Libraries User Guide 49 4 Searching Libraries Customizing a Search Customizing a Search The Library Browser automatically loads all exported spectra into the Spec List window Initiate a library search by double clicking the appropriate entry The search uses the settings defined in the Library Search Options Dialog Box see Figure 35 Figure 35 Library Search Options dialog box Library Search Options Precursor MW IV Mol Weight 50 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Customizing a Search Including a User Library in a Search The default library for a search is the NIST EPA NIH main library mainlid if it is present Otherwise the default is a demonstration user library nistdemo You can add other libraries to the search and change the order of searching on the Libraries page of the Library Search Options dialog box
28. list e Relative mode is not available for Rank or Maxmass types 120 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page parameters Sheet 7 of 7 Parameter Description Other Databases Selection Criteria M Limit the library search to entries in the NIST library also featured in other databases Each entry in the NIST library contains a list of other commercial databases containing information about the compound The data system reports search results featuring in one or more of the selected databases a hit does not have to feature in all the selected databases Fine Report search results from reference compounds or spectra also to be found in the commercially available Fine Chemical Index TSCA Report search results from reference compounds or spectra also to be found in the Toxic Substances Control Act Inventory TSCA RTECS Report search results from reference compounds or spectra also to be found in the Registry of Toxic Effects of Chemical Substances RTECS EPA Report search results from reference compounds or spectra also to be found in the Environmental Protection Agency EPA Environmental Monitoring Methods Index USP Report search results from reference compounds or spectra also to be found in the US Pharmacopoeia USP U S A N HODOC Report search results from reference compounds or spectra
29. m z In a Normal Rank or Maxmass type constraint type the m z value of the mass spectral Thermo Scientific peak to be constrained in this box The data system discards a library hit if it does not contain a mass spectral peak at the specified m z value In a Loss type constraint use this box to type the value of a neutral loss The application discards a library hit if it does not feature a fragment ion at an m z value appropriate to the specified neutral loss in relation to the molecular ion Creating and Searching Libraries User Guide 119 C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page parameters Sheet 6 of 7 Parameter From Description In a Normal Loss or Maxmass type constraint type the minimum abundance of the constrained mass spectral peak in this box In a Rank type constraint you use this box to type the lowest position of the ion in an intensity ordered list of spectral peaks You can specify the same number in both From and To boxes In this case the Xcalibur data system discards a library hit unless the designated mass spectral peak is present in exactly the specified abundance or rank in the retrieved spectrum To In a Normal Loss or Maxmass type constraint type the maximum abundance of the constrained mass spectral peak in this box In a Rank type constraint type the highest position of the ion in an intensity ordered list of spectral peaks in this b
30. of interest Histogram A graphical display of the number of matches as a function of the match factor Click a bar to change the information displayed in the other windows Search results Hit list A list of compounds in the database with spectra that are similar to the unknown Plot of Search Spectrum The plot of the spectrum being investigated Text of Search Spectrum Text about the spectrum being investigated Difference Compare Result A graphical display of peaks from the first often upper spectrum and the second often lower spectrum along with the difference Plot of Hit The spectrum of a search result Hit Text Information Text concerning an item from the search results Figure 2 Library Search window Search Spectrum plot Search Spectrum text rs es 3 Compare window 2 NIST MS Search 2 0 Ident Presearch Default InLib 543 100 spectra File Search Yiew Tools Window Help E x SOG bESax et To a 1 2 Pyrolidinone 1 methyl i AIR Name 2 Pyrroldirore methyH a Formula C 5H NO MW 99 CASH 872 50 4 NIST 1024 ID 2 DB History Other DBs None 10 largest peaks 99999 44929 42840 98689 28 41474 15290 43256 27228 391 Synonyms 1 M Pyrol SA lt j gt Spec list Imainib repib 174948 totalspectra Histogram ici 1000 900 800 700 600 500 lib Match Rm
31. responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A January 2009 Revision B September 2010 Revision C January 2011 to reflect Microsoft Windows 7 compatibility Revision D May 2011 Revision E August 2012 Software version Thermo Xcalibur versions 2 1 2 3 For Research Use Only Not for use in diagnostic procedures B Contents Pr tate ee er Teer ce eer eee vii Related Documentation ssu uu ds Mees oe be eas Kee eo eee Od vii Safety and Special Notes ci cduncosiue can shee anced eaacie aie nots viii Contacting US 2s i200 cpanuiie eae oad tiaa bat hae dae eew ade wae ean ix Chapter1 Overview of Library Browser 02 ccc cece cece tence eee eens 1 Library Browser Process Overview 0 2 00 0c cece nce e eee e eee eens 2 About Library Browser iso oo isis ped be e4iw ee bese Seen wend e ee we 3 Library Browser Windows cs5cniccieas denies trier ieheieenncanes 4 Library Search WINdOW aha edbe ied oe OI OER aOR eee 5 Other Search Window cies cea aeee sae ea
32. single sheet of paper Include spectrum plot in report Include spectrum text of intensities and masses in report Draw structure in plots Add a molecular structure to the spectrum plot if this is available Apply maximum spectrum length Return focus to caller upon completion Provide an upper mass limit for printed spectrum Used in the context of an instrument control program calling the search program Automatic search on Limits Page Carry out a library search automatically in Library Browser when a spectrum is exported from Qual Browser Use the Limits page to define limits for a library search Table 8 Limits page parameters Parameter Apply limits Description Apply limits to the library search Minimum Abundance Specify the minimum level of abundance before including in a search Minimum m z Specify the minimum level of abundance before excluding from a search Maximum m z Specify the maximum level of abundance before excluding from a search Set Default Set parameter values as the default for future searches 114 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Library Search Constraints Page Library View Use the Constraints page to define additional constraints on the search For example limit the search to only compounds with names containing specified letters such as ol for
33. steroidMSMSis C pitcon trial2 C pitcon trial2 steroidMSMSis Qualitative Peaks NL 9 20E5 TCF c Full ms2 MS steroids15 1 99 1 39 3 15 2 47 2 76 1 0 1 5 2 0 3 0 3 5 Time min Thermo Scientific Creating and Searching Libraries User Guide 93 A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 15460 RT 0 68 P NL 114E5 T CFul ms2 363 30 40 00 150 00 375 00 327 0 me 223 2 156 8 1853 197 1 209 1 100 120 40 0 180 200 220 240 260 280 300 320 340 360 Difference Spectra R awda Libray entry 203 297 229 231 247 967 271 284 Relative Abundance 10 0 200 220 240 260 280 300 320 340 378 m z Library Spectrum of Most Probable Hit St 772 RY 776 MSZTEST Entry 1 CAS NA HycdrocortisoneMs2 100 ati 327 2 g 8D g Za 2o 267 lt o 249 251 A Fl oy 2 9 345 3 in P O7 P at 2 157 23 9 315 0 l B 1346 363 37 1 200 20 300 350 m z Table of Results RT 0 68 0 68 0 68 0 68 Scan 23333 Probability 98 82 0 98 0 15 0 00 Name HydrocortisoneMS2 ProgesteroneM 2 DeoxycorticosteroneMS 2 MethyltestosteroneMS2 Sl 772 398 333 275 RSI 776 620 482 437 CAS NA NA NA NA 94 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data Steroids 6 117 RT
34. 2 Right click the entry and choose Copy from the shortcut menu 3 To paste the desired spectra in the top pane go to the Compare window and use the Paste command on the shortcut menu 10 Creating and Searching Libraries User Guide Thermo Scientific 1 Overview of Library Browser Library Browser Windows Formatting the Compare Window To format the compare window Right click in the pane and choose Properties from the shortcut menu The Compare Tool Properties dialog box opens Figure 6 Compare Tool Properties dialog box Compare Tool Properties Plot Comp Result Comp List V Insert best library search hits 3 MV Overwrite contents of the list J No Structures ai 3 7 Spectraperpage Peak Width 11 Legend I Molecular Weight MV Names I CAS Number I Formula Wrap Legend m Color Settings Title Scale plot Peaks plot m Font Settings Oe OOOO Set for all views NIST Sans Serif x E x Regular x Cancel Apply Help You can use the Compare Tool Properties dialog box to change parameters for these options e Plot page Specify plot view parameters Comp Result Specify compare view parameters e Comp List Specify compare list parameters Insert best library search hits Automatically inserts the number of hits specified from the top of the hit list to the compare list Overwrite contents of the list automatically overwrites the current contents of the
35. 5 for more information IMPORTANT For MS MS and MS spectra however do not delete any of the masses that the data system detects because the presence of a particular mass to charge ratio rather than its intensity is essential to identifying a compound Finally the Xcalibur data system provides three ways to search libraries and print custom reports e Automatically by using raw raw or result rst files in Sequence Setup See Setting Up to Search Libraries Automatically on page 64 for more information e Manually by using a single spectrum in Qual Browser See Initiating a Library Search from Qual Browser on page 77 for more information e Manually by using a single spectrum exported to Library Browser See Searching a Library Using Library Browser on page 80 for more information You can use the Qual view options in the Processing Setup window to specify a processing method to print reports automatically Then reference this processing method to specify a sequence of files in Sequence Setup When you process a sequence the data system prints the reports Refer to the Acquisition and Processing User Guide for more information about using Processing and Sequence Setup You can also create processing settings to automatically add spectra to the library If you manually search for search results that match a single spectrum print the results by using the File gt Print command in Qual Browser or in Librar
36. Box see Figure 34 Also use this page to copy a library to another location Figure 34 Convert libraries page F Xcalibur Library Manager CIS GCOZITS 40 lib Ornnwee LI OVI ST 2 J nelude feplicate entes tram tre NIST bran in tre target library BIGWSE To convert a library from one format to another 1 In the Xcalibur Library Manager dialog box type the following information in the Source Library Details area e Select the type of source library based on the file extension from the Type drop down list e Type the path to the source library in the Library field or click Browse to open the Browse for Folder dialog box and find a file e To convert only certain entries from the source library type the number range of the entries to convert in the Process Entries field For example to convert only entries 100 to 200 type 100 200 46 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Converting Libraries to Another Format 2 Enter the following information in the Target Library Details area e Select the type of target library based on the file extension from the Type drop down list e Type the path to the target library in the Library field or click Browse to open the Browse for Folder dialog box and find a folder Note When you select NIST as the target library type the default target library is the library folder for Xcalibur soft
37. Chromatogram view filtered Spectrum view averaged Browser steroids14 steroids14 raw le Edit View Display Grid Actions Tools Window Help C xcalipurexamples data steroids 14 2 28 1996 12 18 18 PM RT 0 00 3 78 E steroids14 51 72 RT 0 59 0 78 AV 22 SB 29 0 39 0 59 0 90 1 11 NL 5 78E4 g a 0 87 NL F c Full ms2 363 30 40 00 150 00 375 00 2 34E6 T004 3082 3074 90 TIC F Full ms2 904 363 30 40 00 150 00 375 00 MS steroids14 80 804 70 704 60 604 50 40 Relative Abundance Relative Abundance a 3 1 30 4 209 2 225 1 239 2 183 1 497 1 1328 0 345 8 373 5 0 0 0 5 10 1 5 2 0 25 3 0 3 6 150 200 250 300 350 Time min miz steroids14 Start S 1 End S 323 fe BT 0 00 3278 55 si a Start Time 0 00 End Time 3 77 100 i b 34E6 Full ms2 303 30040 00 100 00 310 00 90 pi c Full ms2 315 30 40 00 100 00 320 00 80 Ey saidcia Full ms2 331 30 40 00 100 00 350 00 amp 70 c Full ms2 363 30 40 00 150 00 375 00 2 60 3 50 2 40 Z 30 347 349 20 3 23 10 3 30 of 0 27 0 47 EF 0 0 0 5 1 0 15 2 0 25 3 0 3 5 Time min Time 1 04 Intensity 2 06e 005 Scan Filter none Num Scan Filter view Chromatogram view unfiltered 3 To display the scan filter data click the lower left cell and choose View gt Scan Filters The cell lists the filters contained in the total ion current TIC chromatogram over a specified
38. DBs RTECS Contributor Patti Price Georgia Bureau of Investigation Decatur Georgia 10 largest peaks 44999 182500 167159 181 77 183 51 151 39 42 38 77 38 148 37 139 32 Synonyms 1 aw hbnthulennee m inn Thermo Scientific 1 Overview of Library Browser Library Browser Windows Name Search Window R To search a NIST library for a compound name or a text fragment 1 In the Name Search window type a search name into the box in the top left corner of the window for example PACETO see Figure 4 The Xcalibur data system displays spectrum structure and text information in panes in the Name Search window 2 Right click an entry Choose Library Search from the shortcut menu The Browser loads details of the compound into the Compare window and the Plot Text Compare and Hit List panes of the Library Search window The default name search mode accepts both alphabetic a z and numeric 0 9 characters Punctuation and spacing are ignored for example butene is equivalent to I butene Greek characters must be spelled out for example alpha Figure 4 Name search window E Name search PACETO Clear az mainib v p Acetanisidide 2 ritro a p Acetophenetide p Acetophernetidide p Acetophenetidide N hydroxy p Acetopheretidine p Acetopheretitide prAcetoxyacetophenone p Acetox ybromobenze ne p Acetoxytoluene p Acetpheretidin plAcetykming phenol p Acetybriine 20 30 40 50
39. Edit Change Actions View GoTo Help apex Ole pelele elo masma Slalom 2 Sample Type File Name Sample ID Proc Meth Position Inj Vol Level steroids14 Sample14 C Xcalibur examples data_C calibur examples methods steroid C Xcalibur examples methods steroidsMS2 11 20 00 Sample15 C Xcalibur examples data__C Xcaliburexamples methods steroid C Xcalibur examples methods steroidsMS2 12 20 00 0 00 For Help press F1 NUM 6 30 99 2 44PM NOT SAVED 4 8 Repeat Steps 4 and 5 for all other rows of the sequence Step 6 is repeated automatically for subsequent rows 9 To save the sequence list file choose File gt Save As The File Summary Information dialog box opens Type a description in the Comment box and click OK Figure 59 File Summary Information dialog box File Summary Information Header Created Tuesday January 19 1999 10 52 16 AM Modified Tuesday January 19 1999 10 52 16 AM Last saved by tichp Number of saves 1 Comment Cancel Help The Save As dialog box opens 10 Type a name in the File Name box to name the sequence 11 Click Save to save the sequence list and return to the Sequence Setup window 74 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Processing Raw Files and Printing Reports Processing Raw Files and Printing Reports To batch process raw data and print reports automatically use Sequence Setup Whether you are proces
40. Reports on page 87 for an example of library search results initiated from Library Browser Thermo Scientific Creating and Searching Libraries User Guide 85 a B Library Sample Reports This appendix contains samples of possible results using Xcalibur Library Browser Contents e Reports from a Library Search Using Sequence Setup e Report from a Library Search Using Qual Browser e Report from a Library Search Using Library Browser Reports from a Library Search Using Sequence Setup The Xcalibur data system prints reports library search reports automatically from Sequence Setup Click the report name to view an example report e Library Search Report 1 Spectrum of Raw Data 1 Spectrum of Raw Data 2 Spectrum of Raw Data 3 Spectrum of Raw Data 4 Library Search Report 2 Spectrum of Raw Data 1 Spectrum of Raw Data 2 Spectrum of Raw Data 3 Spectrum of Raw Data 4 Thermo Scientific Creating and Searching Libraries User Guide 87 A Library Sample Reports Reports from a Library Search Using Sequence Setup RT 0 00 3 78 SM 7G 1 0 67 Relative Abundance an 0 0 0 5 Qualitative Peaks 1 0 1 5 2 0 Time min 25 3 0 Library Search Report Sample Name Sample 4 Operator jacke Acquisition Date 02 28 96 Run Time min 3 78 Scans 323 Acquisition Time 12 15 58 Dil Factor 1 00 Revision 1 1 beta 1b Low Mass m z 100 00 High Mass m z 375 00 Vial 14 Samp Vol
41. S Compound Identification Automated Compound Identification Using AMDIS Table 1 Library and Settings pane parameters Area Control panel button names Function options Analyze Open a window to select the type of analysis the data file to be analyzed the target library file and the calibration data or library Help Open Help for the Results window Done Close the window Confirm Open the Confirm window Print Print different reports and information Load Results Select and display the results of a previous analysis Results pane area functions R T View the retention time for each chemical N Identifications View the name of the compound found Component View the component parameters for the deconvoluted chromatographic peak Match View the match factors between the mass spectrum of the component and that of the library Library and Settings pane views Library Examine the library Spectra Compare the library spectrum with the extracted spectrum Settings Examine the settings for the analysis Standards View the retention index standards and internal standards QA QC or S N Examine the QA QC report or the S N for the run Options Set options for the printed results 104 Creating and Searching Libraries User Guide Thermo Scientific Confirm Window Thermo Scientific B AMDIS Compound Identification Automated Compound Identification Using AMDIS The Confirm wind
42. ST libraries Delete EEN pe Archive Thermo Scientific Creating and Searching Libraries User Guide 43 3 Managing Libraries Managing the NIST Libraries Adding a Library When you add a library to the NIST libraries list either copy the library file to the local computer or link to the library at a remote location without copying files bd 1 Deleting a Library To add a library In the Library Manager Dialog Box click Add The Add Library dialog box opens see Figure 32 Figure 32 Add Library dialog box Add Library Source es Browse Action Copy the library to the local computer Link to the library from either a remote location or computer Cancel In the Add Library dialog box type the path for the new library file in the Source field or click Browse to bring up the Browse for Folder dialog box and find the desired file Select one of the two options e Copy the library to the local computer e Link to the library from either a remote location or computer Note Because libraries can be large you can often save time by selecting the Link option rather than the Copy option Click OK The data system adds the desired library to the NIST Libraries list in the Xcalibur Library Manager dialog box If you have no more tasks to complete with the Library Manager click Exit To delete a selected library in the NIST Libraries list In the Xcalibur Library Manag
43. T 0 01 AV 1 NL 2 14E3 e A comment showing the Scan Filter such as T c Full ms2 363 30 150 00 375 00 e The Mol Weight and CAS Number fields are set to zero You might want to modify the basic information or provide the following e A chemical formula e A list of synonyms The molecular weight e The CAS number e A chemical structure in MOL SDE or MDL file format To edit a library entry see Editing a User Library on page 30 24 Creating and Searching Libraries User Guide Thermo Scientific ee ie Managing Libraries Library Browser can create manage and search user libraries Use these functions to create reference libraries from your own spectra Use the Xcalibur data system to create a custom library of MS MS spectra The data system includes a subset of the NIST mass spectral library called nistdemo The NIST EPA NIH main library contains more than 100 000 compounds whose MS type spectra were obtained primarily in electron ionization EI scan mode You might want to create a custom library that includes MS MS spectra or spectra of MS analyses Contents e Creating a User Library e Adding Spectra to a User Library e Editing a User Library e Managing the NIST Libraries e Converting Libraries to Another Format Thermo Scientific Creating and Searching Libraries User Guide 25 3 Managing Libraries Creating a User Library Creating a User Library You can create a user library in two ways expo
44. Thermo Scientific Creating and Searching Libraries User Guide 91 A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 268 RT 3 17 P NL 7 8564 T cFul ms2 315 90 40 00 00 00 320 00 297 1 239 0 10 20 40 160 0 200 220 240 260 280 300 320 340 360 Difference Spectra R awdota Libray entry Relative Abundance w Wo 0 B0 200 220 240 260 280 300 32C mz Library Spectrum of Most Probable Hit SI 769 RSI 769 MSZTEST Entry 4 CAS NA ProgesteroneMS2 Relotive Abundance Table of Results RT Scan Probability Name SI RSI CAS 3 17 268 98 61 ProgesteroneMS2 769 769 NA 3 17 268 0 98 HydrocortisoneMS2 403 404 NA 3 17 268 0 33 DeoxycorticosteroneM 2 379 463 NA 3 17 268 0 00 MethyltestosteroneMS2 329 386 NA 92 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Reports from a Library Search Using Sequence Setup Sample Name Acquisition Date Acquisition Time Low Mass m z Samp Vol Comments Inst Method Proc Method Data Path RT 0 00 3 76 SM 7G 100 90 80 70 60 50 40 Relative Abundance 20 10 0 0 0 68 0 30 0 5 Library Search Report Sample15 Operator jackc 02 28 96 Run Time min 3 75 Scans 313 12 21 31 Dil Factor 1 00 Revision 1 1 beta 1b 100 00 High Mass m z 375 00 Vial 12 0 00 Samp Wt 0 00 Inj Vol uL 20 00 C pitcon Mtrial2
45. actor gt 900 and the next best hit has a match factor of 300 the probability of the compound being correctly identified is high Conversely if several hits are returned with very similar SI matching factors the probability of a correct assignment is low Shows the formula structure molecular weight name and library index number of the currently selected hit in the Hit List Compares the submitted spectrum with the currently selected library spectrum in the Hit List Peaks above the X axis are relatively more intense in the sample than the library entry Negative peaks are relatively more intense in the library entry than in the sample spectrum Displays the submitted spectrum above the currently selected library spectrum in the Hit List Note Avoid making positive assignments based solely on the statistical result of a library search The Xcalibur data system might identify a compound with an unusual structure or more importantly an unusual mass spectrum in a definitive way More usually your unknown might be a member of a class of compounds with very similar mass spectra The ability of Qual Browser or any search system to distinguish between them is limited In many cases the best that the search algorithm can do is identify a class of compounds that have similar mass spectra and usually similar structure In most cases you should seek confirmation by other analysis techniques 124 Creating and Searching Libraries User Gu
46. also to be found in the CRC Handbook of Data of Organic Compounds HODOC NIH Report search results from reference compounds or spectra also to be found in the NIH NCI Inventory File EINECS Report search results from reference compounds or spectra also to be found in the European Index of Commercial Chemical Substances EINECS IR Report search results from reference compounds or spectra also to be found in the NIST EPA Gas Phase IR Database Clear All Clear all the check boxes in the Other Databases area Button Save As Default Thermo Scientific Validate and save the settings on the current page as default settings The data system uses these settings for all new processing methods overriding the previous default values permanently Creating and Searching Libraries User Guide 121 C Library Reference Spectrum Information Dialog Box Spectrum Information Dialog Box Use the Spectrum Information dialog box to type or to change information stored with a library spectrum The dialog box displays information for the spectrum selected in the Spec List in the Librarian window Figure 74 Spectrum Information dialog box Spectrum Information Name 2 Pyrroidinone 1 methyl m Peak information m Formula C5H SNO From structure m Other Names Synonyms M Pyrol N Methyl alpha pyrrolidinone N Methyl alpha pyrrolidone N Methyl gamma butyrolactam N Methyl 2 pyrrolidinone Comments Mol weight 39 ID
47. and return to the Spectrum Information dialog box see Figure 24 click Accept Figure 24 Spectrum Information dialog box showing the structure to add Spectrum Information hydrocortisoneMS2 36 Creating and Searching Libraries User Guide Thermo Scientific Thermo Scientific 10 3 Managing Libraries Editing a User Library g Click Add to Library to display the Choose Library to Save to dialog box see Figure 25 Figure 25 Choose library to save to dialog box Choose libraytosaveto O Choose libraytosaveto O to save to r List of libraries nistdemo Cancel i Help Library Statistics Spectra ID h To save the structure to the library click OK The application closes the Choose Library to Save to dialog box and opens the Librarian window The source of the entry appears as the new library name Highlight the entry in the Spec List The Text File designation appears in the Plot pane To delete the entry click X in the toolbar A warning appears Click OK to close the warning dialog box Click the Lib Search tab to return to Library Browser s Library Search window Double click the entry in the Spec List The data system attaches the chemical structure to the library entry Creating and Searching Libraries User Guide 37 3 Managing Libraries Editing a User Library Adding Additional Compounds to the User Library To add compounds to a use
48. and select from the three available conditions lt less than gt greater than or equal to 3 In the same row click the Value box Type the required number of elements for the element constraint condition 4 Repeat Steps 1 3 on the next available row to add further elements to the table 60 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Limiting a Library Search To use the Elements in Compound constraints 1 Select the Elements box and type the IUPAC approved abbreviation for each element see Figure 45 that must be present in returned search results Separate each element in the list of up to 30 characters by the character specified as the list separator character Refer to Changing the List Separator Character in Chapter 2 in the Acquisition and Processing User Guide for more information 2 Select the All option to have the returned search results contain all and only the listed elements For example C H O would return HCHO but not CO3 CH4 or CHCl 3 Select the Some option to have the returned search results contain at least one of the specified elements and no elements other than those listed For example C H O would return CO CHy and HCHO but not CH Cl Cl not allowed If you leave the box blank the data system does not apply the Elements in compound constraint function If you type an invalid element the data system reports an error when th
49. aries Creating a User Library 1 To create a library from the Library Browser window 1 Select a spectrum in the Library Browser window 2 In the Librarian window click eal in the toolbar to display the Spectrum Information Dialog Box see Figure 15 Figure 15 Spectrum Information dialog box Spectrum Information Name steroids1 4250 284 RT 2 98 3 31 AV 3 r Formula From structure r Other Names Synonyms Comments IF c Full ms2 315 30 40 00 100 00 32 Mol Weight jo ID Number 2 CAS Number jo Peaks 129 Library Text File Add to Library Replace Add to List Attach Struct Clipboard Struct CRUE No structure Exit Help 3 Click Add to Library to add the spectrum to a new library and name the library The Choose Library To Copy To dialog box opens Thermo Scientific Creating and Searching Libraries User Guide 27 3 Managing Libraries Creating a User Library Click the Libraries tab to display the Available Libs and the Included Libs list of libraries see Figure 16 Figure 16 Library Search Options dialog box Library Search Options Spectrum search 5 Type the name of the new user library 6 Click OK to create the new user library and close the dialog box 28 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Adding Spectra to a User Library Adding Spectra to a User Library Use the Append to User Library area show
50. as been designed for MS data and has superior peak detection efficiency at low MS signal levels This is the Xcalibur default peak detection algorithm Genesis This algorithm is the original Xcalibur peak detection algorithm and has been provided for backward compatibility with Xcalibur 1 0 data system studies Avalon This algorithm supports detectors other than MS and detects negative chromatographic peaks and shoulders more accurately than Genesis or ICIS 5 In the Filter list select a scan filter 6 To accept current changes to the Identification page click OK 7 To set advanced parameters click the Advanced button see Figure 49 Note For the following procedure the ICIS Advanced Parameters dialog box opens If you choose another peak detect method a different Advanced Parameters dialog box opens Fill in the values that are appropriate for the method a Confirm that the INCOS Noise option is selected in the Noise Method area Figure 49 ICIS Advanced Parameters dialog box ICIS Advanced Parameters 66 Creating and Searching Libraries User Guide Thermo Scientific Thermo Scientific 4 Searching Libraries Setting Up to Search Libraries Automatically Note The Xcalibur data system generates the Available Libraries list dynamically Each time you open the Search List dialog box The application lists the libraries available on the system at that time Libraries listed in the Selected Libraries lis
51. atch Prob Name i xi i E 999 999 9740 DPW Ee 10 20 30 40 50 60 70 a0 90 100 110 Search Results m2 R 928 950 974 2 Pyr Ya 2 Pyrraldinore methy Difference hu 2 P rraidinone methyH list ms R 923 935 97 4 2 Pyr Difference A_Head to Tail A Side by Side_ Subtraction _ 999 999R 97 4P a a ae a Hist aie Name 2 Pyrroldinone methyt b m 754 765 027 1Pyr Formula C5H9 NO F 7 a R ma 72 010 2 Pip MW 99 CASH B72 50 4 NISTH 1024 ID 52875 DB r m8 R 725 726 00B Piperi Tip gest peaks m M a7 ae 00 Pipan 99999 44929 42840 9B BP 28 z P 1 a o foe 41474 15290 43256 27228 391 2 Synonyms m2 R 705 706 004 Piperi 1 MPyol mia R 702 703 006 Piperi a age a ae 2 N Mtethy a pyrroldina 3 lt amp mainib 2 Pyrroidinone 1 methy lt l gt InLib 543 Hit List For Help press F1 Ident dent _ ednesday February 02 2005 Hit plot Hit text Thermo Scientific Creating and Searching Libraries User Guide 5 1 Overview of Library Browser Library Browser Windows Using the Spec List The Library Browser stores spectra in the Spec List pane of the Library Search window when you do either of the following e Export spectra from Qual Browser e Import spectra from other sources using the File gt Open command e Geta spectrum from a library The Browser identifies the origin of each Spec List entry with an initial letter T Spectra that came directly from a text file such as t
52. brarian window click I in the toolbar The Spectrum Information dialog box opens see Figure 22 Figure 22 Spectrum Information dialog box Spectrum Information Name hydrocortisoneMS2 Formula From structure Other Names Synonyms Comments IF c Full ms2 363 30 40 00 150 00 37 Mol Weight jo ID Number 2 CAS Number jo Peaks 145 Library ms2test Add to Library Replace Add to List Attach Struct Clipboard Struct SMEA No structure Exit Help b To search for chemical structure files from other sources click the Attach Struct button The Open dialog box opens 34 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Editing a User Library c Ifthe structure you want is not available in the Open dialog box folders click Cancel to search other libraries The Attach Structure to User Spectrum dialog box opens see Figure 23 Figure 23 Attach Structure to User Spectrum dialog box Attach Structure to User Spectrum user file d Select a library name in the Get Structure From area and click Open Library e Type the name of the compound to search for in the Substring Search box Then click Substring Search Library Browser scans the library and finds the MS data and the structure for your entry Thermo Scientific Creating and Searching Libraries User Guide 35 3 Managing Libraries Editing a User Library f To accept the structure
53. brary Search Option Parameters Setting Library Search Option Parameters Use the Library Search Options page see Figure 38 to specify how the library search is carried out To set Library Search Option parameters 1 Open the Search Parameters Page of the Search Properties dialog box From the Qual Browser window choose Actions gt Library gt Options or right click within a Spectrum view and select Library gt Options from the popup context menu Click the Library Search Options tab Figure 38 Library Search Options page from Qual View Identification Spectrum Enhancement Library Search Options Library Search Constraints Search type Append to user library Mass Defect Identity C Similarity V Enable l Enable Normal J User library C Quick C steroids Penalize rare compounds g Thresholds Options Match factor o J Maximum number of hits 5 Reverse match factor jo Reverse search Probability 9 V Search with Mw I robability 7 Cancel Save As Default Search List Help 2 To submit processed spectra to an identity search select an Identity option in the Search Type area Figure 39 Search type area default settings Search type 3 C Similarity Normal O Quick Fe C Penalize rare compounds te 3 Choose one of the three Identity search types e Select the Normal option to use a normal identity search e Select the Quick option to use a quick identity search e Select th
54. ce Library Manager Dialog Box Manage Libraries Page Use the Manage Libraries page to add a library to the NIST libraries list or to delete a library from the NIST libraries list You can also copy a library to another location Table 4 Manage Libraries page parameters Sheet 1 of 2 Parameter NIST Libraries Description NIST Libraries list View all of the NIST libraries currently available on your computer or network You can add libraries to this list delete libraries from this list and copy libraries on the list to another location Buttons Add Add a library to the NIST Libraries list The Add Library dialog box opens The Add Library dialog box has the following parameters e Parameter e Description e Source Use this button to specify the location of the library that you want to add Copy the library to the local computer Select this option to copy the selected library to your computer Linkto the library from either a remote location or computer Select this option to access the library remotely Note Because libraries can be large you might save time by using the Link option rather than the Copy option Click OK when you have selected the library you want to add and selected Action options Delete Delete the library that you have previously selected in the NIST Libraries list Select the library that you want to delete from the NIST Libraries list Click Delete The Delete Libra
55. ce h FS x Pas pou Pras Piri pate i co 150 20 250 300 373 mye 98 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Report from a Library Search Using Library Browser Report from a Library Search Using Library Browser This section includes an example report of a library search that you can print from Library Browser 50 Q OH 150 220 290 360 U HydrocortisoneMS2 981R 98 8P U Hydroc 454 651R 0 98P U Proges 383 523R 0 15P U Deoxy 343 344R 0 03P U Hydroc 0 01P U Methylt 311 336R 0 00P U Aldost 296 303R 0 00P U Colchi 282 321R 0 00P U Folic A 270 337R 0 00P U 17 alp 10 266 266R 0 00P U Reserp 11 266 555R 0 00P U Hydroc 12 259 306R 0 00P U Distan 13 246 432R 0 00P U Squala 14 244 378R 0 00P U Diethyl 15 244 329R 0 00P U Ergota 16 233 470R 0 00P U Sulfiso U HydrocortisoneMS2 T steroids14 51 75 RT 0 Conan e ONI wo j pg w te 2 HydrocortisoneMS2 Formula MW NA CASH NA NIST NA ID 1 345 DB ms2test 73 _ Comment F c Full ms2 363 30 150 220 290 360 171 Masses and Abundances U HydrocortisoneMS2 150 11 247 96 15t 51 248 17 153 3 249 397 154 16 250 20 155 641 251 380 156 281 252 4 157 135 253 156 158 61 254 10 159 109 255 21 l l 160 Tr 256 8 161 57 257 25 162 1 258 27 163 21 259 164 Tr 261 165 9 262 166 4 263
56. ch results are reported and appends the searched spectrum to the specified library Unless otherwise specified the library is stored in the NIST MSSearch folder Thermo Scientific Creating and Searching Libraries User Guide 29 3 Managing Libraries Editing a User Library Editing a User Library To edit a user library entry that contains an MS MS spectrum exported from Qual Browser use the following procedure To edit a user library complete the following tasks detailed in this section e Editing Spectrum Information e Attaching a Chemical Structure to a Library Entry e Adding Additional Compounds to the User Library Editing Spectrum Information To edit MS MS spectrum information in Library Browser 1 Open Library Browser and choose Window gt Librarian The Librarian window opens Because the information for an MS MS spectrum is stored as a text file the source of the data is listed as Text File in the Plot Text pane see Figure 18 Figure 18 Librarian window showing the spectrum information as a text file 3 NIST MS Search 2 0 Librarian m File Search Yiew Tools Window Help le x e Stee Sjaal Dfe x a i _ Ste Name 1004 309 327 1 A sterol 267 504 281 291 150 170 190 210 230 250 270 290 310 330 350 370 Text File steroids 4451 72 RT 0 59 0 78 AV 22 SB 29 0 39 0 59 0 90 1 11 Name steroids 4451 72 RT 0 59 0 78 AV 22 SB 29 0 39 0 59 0 90 1 11 Formu
57. click this entry and choose Copy from the shortcut menu d To make the Spec List pane active move the cursor to the Spec List pane and left click the mouse button e To paste the entry to the Spec List window right click to display the shortcut menu and choose Paste 40 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Editing a User Library 8 Choose Window gt Librarian to display the Librarian window see Figure 29 Figure 29 Librarian window showing the entry from the source file highlighted NIST MS Search 2 0 Librarian alx 129 283 301 100 120 140 160 180 200 220 240 260 280 300 Text File steroids 4 1 13 129 _RT 1 32 1 47 AV 17 NL 2 33E4 Name steroids 4 113 129 RT 1 32 1 47 AV 17 NL233Ed Formuka MW N A CASH N A NISTH N A ID 9 DB Text File Other DBs None Comment T c Full ms2 331 30 40 00 100 00 350 00 10 largest peaks 295999 277755 109723 253714 313498 271 405 213399 221387 225375 171375 Synonyms ne synonyms Thermo Scientific Creating and Searching Libraries User Guide 41 3 Managing Libraries Editing a User Library 9 To delete the entry highlight the entry from the source file and click x in the toolbar see Figure 30 Figure 30 Librarian window showing added entries NIST MS Search 2 0 Librarian laf x 267 281 291 209 150 170 190 210 230 250 ms2test hydrocortisone 52
58. d Compound Identification Using AMDIS Results Window The Results window contains only search results and is most commonly used for routine analyses see Figure 72 Figure 72 AMDIS Results window AMDIS Results TEST D C NISTO2 4MDIS32 DATASHPSTEST R T min 8 Identifications have been made Soman GD Diisopropyl methylphosphonate DIMP 2 Nonanal Tabun GA Cyclohexy methylphosphonofluoridate GF Undecane Confirm Print 4 99 m z Load Results Min Abund 0 039 Library Spectra Settings Standards GA QC S N Options 16 Compounds in C NISTO2 4MDIS32 LIB GROBX MSL 77816 Sarin GB 87 62 7 Synonyms 95 78 3 D Isopropyl methylphosphonofluoridate 96 64 0 O lsopropyl methylfluorophosphonate 101 83 7 Phosphonofluoridic acid methyl isopropyl ester TEPE 0 2 propyl methylphosphonofluoridate v 111 820 J Formula C4H10FO2P Rl Class TAT The Results window is divided into three areas the Control panel top left the Results pane top right and the Library and Settings pane See Table 1 Use the Library and Settings pane to e Examine the library e Compare the library spectrum with the extracted spectrum e Examine the settings for the analysis e View the retention index standards and internal standards e Examine the QA QC report or the S N for the run e Set options for the printed results Thermo Scientific Creating and Searching Libraries User Guide 103 B AMDI
59. d Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page parameters Sheet 5 of 7 Parameter Description Type Specify the type of ion constraint Normal Applies to a specific ion represented by its m z value The From and To values represent the abundance of the ion Loss Describes a neutral loss from a molecular ion In this case the m z value limited to 64 represents the mass of the lost neutral group for example for methyl m z 15 For this constraint to be matched a library spectrum must contain the following e A fragment ion at an m z value 15 less than the molecular ion e An abundance in the specified From and To range Rank Tests the order of an ion in the spectrum in terms of relative abundance Ions are ranked from the largest the base peak to the 16th A compound matches a Rank constraint if its library spectrum contains a mass spectral peak with these criteria e At the specified m z value e Ranked between the specified From and To rank positions If you specify the same number in both fields the designated ion must have that rank in the retrieved spectrum Maxmass Sets a constraint on the m z value of the most significant high mass ion Library search results must feature the following e An ion at the specified m z value e No significantly larger masses at higher m z values e An abundance in the specified From and To range
60. e so CYCLO returns compounds containing the fragments cyclo Cyclo and CYCLO Creating and Searching Libraries User Guide 115 C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page parameters Sheet 2 of 7 Parameter Description Elements Value Individual Element Table Set specific criteria about the elements required in a library hit Each row in the table represents an element constraint Element Condition Value 1 jF gt 5 2 ci 3 There are three parts to each constraint Element An IUPAC approved abbreviation for an element for example Cl for chlorine e Condition A mathematical operator lt less than gt greater than or equals e Value A numerical value representing the number of atoms of the specified element required to satisfy the constraint In the example shown here the Xcalibur data system only returns search results for compounds that contain more than five fluorine atoms or exactly three chlorine atoms You do not need to provide a complete elemental profile The library search returns compounds if they satisfy all the specified criteria regardless of any other elements present Row Number Enter a new item in the last unused row in the table indicated by an asterisk Each numbered row represents an item in the table Element Type the IUPAC approved abbreviation for the element you want to use an ele
61. e Exporting Spectra Manually from Qual Browser e Exporting Spectra Automatically from the Processing Method For more information see Adding Spectra to a User Library on page 29 Exporting Spectra Manually from Qual Browser To export the enhanced spectrum to Library Browser To export an MS MS spectrum to the Library Browser right click the spectrum view upper right cell and choose Library gt Export to Library Browser Xcalibur automatically displays the Library Browser see Figure 13 22 Creating and Searching Libraries User Guide Thermo Scientific 2 Adding a Spectrum to a Library Exporting Spectra from the Xcalibur Data System Figure 13 Library Search window 3 NIST MS Search 2 0 Ident Presearch Default InLib 1682 100 spectra Elz mef o File Search Yiew Tools Window Help als x eas iE Sne O E ronas RT 233 55 amp Name Name steroids 4 250 284 RT 2 98 3 31 AV 35 SB 4 a sterai Formuk MW N A CAS N A NIST H N A ID 2 DB Text File Other DBs None Comment F c Full ms2 31 5 30 40 00 100 00 320 1 10 largest peaks 297999 279919 109501 255399 223 Structures mainib repib 174948 totalspectra 100 10 1 239 330 215311 227204 253197 159 100 140 180 220 260 300 Synonyms Ml Text File steroids 44250 284 RT 2 98 3 31 AV 35 SB 4 lt u gt Plot Text of S
62. e Penalize Rare Compounds option if you want a modified normal identity search 54 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Setting Library Search Option Parameters 4 To submit processed spectra to a similarity search select the Similarity option Then choose one of the three Similarity search types e Select the Simple option to use a Simple Similarity search e Select the Hybrid option to use a Hybrid Similarity search e Select the Neutral Loss option if you want a Neutral Loss Similarity search The difference between the two search types is primarily in the weightings of the spectrum as a function of mass 5 To limit the number of search results to be returned by a library search and reported in the result file type a number in the Maximum Number of Hits box Figure 40 Options area default settings Options Maximum number of hits 5 Hi Search with Mw 6 Ifyou know the molecular weight of your target analyte and want to restrict the search to library compounds of the same molecular weight select the Search with MW check box and type the molecular weight in the associated box Do not use the Search with MW option when you have already clicked the Molecular Weight option on the Library Search Constraints page 7 To include mass defect values for library searches select the Enable check box in the Mass Defect area 8 Select a sorting method for hits in the resul
63. e box Thermo Scientific Creating and Searching Libraries User Guide 59 4 Searching Libraries Limiting a Library Search Applying Element Constraints To constrain the library search to compounds with specific element profiles select the Enable check box in the Element Constraints area There are two methods e Individual Element e Elements in Compound To use the Individual Elements constraints 1 Click the Element box Type the required element abbreviation Use this area to set specific criteria about the elements required in a library search result hit For example the entries shown in Figure 45 would only return search results for compounds that contain more than five fluorine atoms and exactly three chlorine atoms Figure 45 Element constraints area Element constraints V Enable Individual element Elements in compound Element Condition Value Elements 1 FCI 2 ji J O pee ied You do not need to provide a complete elemental profile The library search returns compounds if they satisfy all the specified criteria regardless of any other elements present Use this option to specify which elements you do not want to be in a library hit For example C 0 confirms that no search results contain carbon When a contradiction occurs for example C lt 2 and C gt 4 the data system displays an error dialog box Correct the contradiction to proceed 2 In the same row click the Condition list Click the arrow
64. e ea pe eKe alias 5 8 Name Search Window tbGoteatednen adie s cienacantesdeuedbns 9 Compare Wind W oi lt inacvied ieee Rie neve Reena ee Reece aR Eea 10 Librarian Window cias eae Koss ieee hehe 12 Chapter2 Adding a Spectrum to a Library 0 ccc cece e eee eee eee eens 15 Opening a Raw Data File in Qual Browser so i4 000 00 seesw sad vaww nes 15 Viewing a Spectrum in Qual Browser lt 4 casa ctd ceed steven cdedete sass 16 Working with Background Spectra 0 eee 18 Using the Subtract Background Tool iis caer ed deeds ea ey ew eea ees 19 Subtracting Background Specttaii since e acne es shone eae hee eed ea 20 Exporting Spectra from the Xcalibur Data System 0 0000048 22 Exporting Spectra Manually from Qual Browser 0 0008 22 Exporting Spectra Automatically from the Processing Method 24 Chapter3 Managing Libraries cece cece eee eeaee 25 Creating a User Library vp cen d ene kenaen ethene i eee Re EEA i E ES 26 Adding Spectra to a User Mibrary ec o0h ced eso ce eee eS eed 29 Editing a User Librafy ced ohn be naw ee aa eo nace panda kaei 30 Editing Spectrum Information soscacikewdccteaxdecd en sasa Sea ceed 30 Attaching a Chemical Structure to a Library Entry 1 d0 irs deswse aes 32 Adding Additional Compounds to the User Library 00 38 Thermo Scientific Creating and Searching Libraries User Guide iii Contents Chapter 4 Appe
65. e edit field loses focus If there are no contradictions you can use the two types of elemental constraints together For example if the Individual Element area contains C 0 or C lt 1 in and the Elements In Compound box contains C when the All option has been selected the data system displays an error dialog box Correct the contradiction to proceed Applying Mass Spectral Peak Constraint Thermo Scientific The Mass spectral peak constraint feature builds a profile of ions and their abundances to be matched against library entries during the search To apply mass spectral peak constraints Select Enable in the Mass Spectral Peak Constraints area The search algorithm only returns search results matching the specified constraints Figure 46 Example of a relative mass spectral peak constraint Mass spectral peak constraints V Enable Type m z From To Absolute 1 Norma 7 0 C Relative 3 0 lt New gt Creating and Searching Libraries User Guide 61 4 Searching Libraries Limiting a Library Search 62 To specify how the data system applies the From and To parameters in the Mass spectral peak constraints table To evaluate all table entries as a percentage of the base largest ion in the spectrum select the Absolute option To treat the first entry as an absolute Normal or Loss type select the Relative option The software considers subsequent entries in the table relative to the first
66. e type of source library to another type of library at a target location and to copy a library to another location Table 3 Convert Libraries page parameters Sheet 1 of 2 Parameter Source Library Details Description Type Source Library Browse Source Choose the source library file type that you want to convert to another file type Select any of the following file types ICIS GCQ ITS 40 lib lbr MassLab idb ANDI MS cdf NIST or AutoMass spr prs nam hdr Choose the source library that you want to convert To change the library click Browse and select the path to the source library on your computer or network Process Entries Source Specify the number range of the library entries that you want to convert from the source library If you leave the box empty the Xcalibur data system converts all entries The format is First Entry Last Entry For example to convert library entry 100 through library entry 200 type 100 200 in the Process Entries box Target library details Type Target View the target library file type when converting the source library If you select source library file type ICIS GCQ ITS 40 MassLab ANDI MS or NIST you can select from the following target library file types ICIS GCQ ITS 40 lib lbr MassLab idb NIST or ANDI MS cdf If you select source library file type AutoMass you can only select the NIST target library file type
67. earch Spectrum Plot of Search Spectrum Plot Text of Spec List Spec List 279 255 297 215 273 sit 123 159 173183 20l a T 1000 900 800 700 600 500 400 300 200 tk COON RHE W NH 433 415 438 433 481 418 482 586 409 444 575 365 376 107 RMatch Prob Name 20 4 20 4 6 82 5 09 4 30 3 63 3 21 2 71 2 39 2 02 186 1 86 1 72 1r 153 174 184 198 212 105115 129 141 242 252 270 284 294 100 312 E i e Re al a Pregn 100 120 140 10 180 200 220 240 260 280 300 320 V2 4 Asteroids 44250 2864 RT 2 98 3 31 A Differerce Vv Pregna 4 7 diene 3 20 diore re Difference K_Headto Tall Side by Side Subtraction 414 433R 20 4P Boran Name Pregna 4 7 diene 3 20 diore Gibb Formuk C21 H2802 9 Oxa MW 312 CAS 17398 60 6 NIST 25073 ID 12252 DB Meth Other DBs None Ent 3 Contributor DENNIS H SMITH DEPT OF C HEM STANFORD Medr 10 largest peaks Bis 1 7 43999 312808 297567 227494 91237 Ethyl h 55178 105163 41161 81145 85142 7 Hyd Synonyms 100 140 180 220 260 300 ne synonyms mainib Pregna 4 7 diene 3 20 dione lt f J gt Compare Librarian Ident Ident l l Thermo Scientific The data system converts the mass and intensity data of the spectrum to a text file and copies the file to the Spec List pane The Qual Browser window stays open The data syste
68. elp ape oly oleae ee aie eh Bl o e gt lalu 2 Sample Type File Name Sample ID Inst Meth Proc Meth Std Bracket steroids14 Sample14 Ee C calibur example C Xcalibursexamples methods steroid 11 20 00 standard Std Bracket Sample15 C calibur examples data C Xcalibur example C Xcaliburexamples methods steroid 12 20 00 standardl 0 00 For Help press F1 NUM 6 30 99 3 52 PM NOT SAVED 7 Note Use Sequence Setup to create a sequential list containing a variety of sample types or brackets However when performing qualitative analysis the type is usually unknown Thermo Scientific Creating and Searching Libraries User Guide 73 4 Searching Libraries Setting Up to Search Libraries Automatically 5 To view the Sample Type column click the left side of the horizontal scroll bar at the bottom of the workspace Double click the Row 1 cell in the Sample Type column to display a drop down list Then scroll up to select Unknown 6 Expand the width of the Path column to confirm that the directory is the one storing the raw files For example raw files containing steroids data are found in C Xcalibur examples data 7 To select the processing method double click the Row 1 cell in the Processing Method column Browse to select the processing method Figure 58 shows the edited list of two files contained in steroid sld Figure 58 Sequence Setup window X steroid sid Open Sequence Setup olx Fie
69. elp from within the software Thermo Scientific Creating and Searching Libraries User Guide vii Preface Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or may contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier viii Creating and Searching Libraries User Guide Thermo Scientific Preface Contacting Us There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To get local contact information for sales or service Go to www thermoscientific co
70. entry complete the tasks detailed below Contents e Opening a Raw Data File in Qual Browser e Viewing a Spectrum in Qual Browser e Working with Background Spectra e Exporting Spectra from the Xcalibur Data System Opening a Raw Data File in Qual Browser To view raw data use the Qual Browser window Open a data file to expand the Qual Browser menu bar To display the raw data of a steroids data file 1 To display the Xcalibur Home Page from your computer desktop double click or choose Start gt Programs gt Thermo Xcalibur gt Xcalibur on the computer desktop To display the Qual Browser window click pa on the Xcalibur Home Page Choose File gt Open or click B in the toolbar The Open Raw File dialog box opens Browse to the location of the raw file and select the file A AR B amp B N Click Open The chromatogram and first mass spectrum for this data file appear see Figure 9 Thermo Scientific Creating and Searching Libraries User Guide 15 2 Adding a Spectrum to a Library Viewing a Spectrum in Qual Browser Viewing a Spectrum in Qual Browser To view a mass spectrum use the interactive cells of the Qual Browser window 1 To display a mass spectrum of the raw data in a window containing four cells 1 Confirm that the data system displays a Chromatogram view similar to Figure 9 If you cannot see the chromatogram view do the following a Select a cell The application shows both the chromato
71. equences and processes refer to the Processes and Sequences User Guide To set up for automatic searching complete the following procedures e Specifying Search Parameters in the Qual View e Specifying Report Options for Library Searches e Specifying Raw Data Files in Sequence Setup 64 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Setting Up to Search Libraries Automatically Specifying Search Parameters in the Qual View To search libraries automatically set up the Qual view in the Processing Setup window For this example use steroids data Note Using the Library Search Constraints page requires specific knowledge about the target compounds in the chromatogram It is not always possible to use this knowledge to refine automated processing To specify parameters for a qualitative library search in the Qual view 1 To open the Processing Setup window from the Xcalibur Home Page click a 2 Open a raw data file in the Qual view a To display the Qual view click i on the view bar b To display the Open Raw File dialog box choose File gt Open Raw File c To display the raw data select a raw file and click Open see Figure 48 Figure 48 Processing Setup window me Processing Setup Qual Identification Untitled Int Std File View Zoom Options GoTo Help Identification Spectrum Enhancement Library Search Options Library Search Constraints Peak Purity
72. er dialog box select a library to delete from the NIST Libraries list Click Delete The system prompts you to confirm the deletion To delete the selected library click Yes If you have no more tasks to complete with the Library Manager click Exit 44 Creating and Searching Libraries User Guide Thermo Scientific Copying a Library 3 Managing Libraries Managing the NIST Libraries You can copy a selected library to another directory on the computer or network by using the Archive feature Thermo Scientific To copy a library In the Library Manager Dialog Box select a library to copy from in the library name in the NIST Libraries list Click Archive The Archive Library dialog box opens see Figure 33 Figure 33 Archive Library dialog box Archive Library Destination Browse Cancel In the Archive Library dialog box type the path for the copied library file in the Destination field or click Browse to bring up the Browse for Folder dialog box and find the desired location To copy the desired library to the remote location click OK If you have no more tasks to complete with the Library Manager click Exit Creating and Searching Libraries User Guide 45 3 Managing Libraries Converting Libraries to Another Format Converting Libraries to Another Format To convert all or any portion of a library to another format use the Convert Libraries Page in the Library Manager Dialog
73. g Libraries User Guide Thermo Scientific 4 Searching Libraries Customizing a Search Searching a User Library Entry by ID Number To search entries in existing libraries search for a library spectrum by Formula ID Number Molecular Weight Any Peaks CAS Number Sequential Method NIST Number or Name Use ID Search if other information is not available or to find a spectrum exported from a processing method To search a library by ID Number 1 To open the ID Number Search dialog box see Figure 37 choose Search gt ID Number from any Library window Figure 37 D Number Search dialog box ID Number Search ID Number or 4 range e g 1 or 1 5 z Library mainlib r Library Statistics 147198 Spectra 1 147200 ID Cancel Help The Library Statistics area shows the number of available spectra 2 To consider all spectra specify a range in the ID Number box that is equal to or larger than the ID range shown in the Library Statistics area 3 Select the appropriate user library in the Library drop down list 4 Click Search The Xcalibur data system writes all entries within the specified range to the Lib Search area 5 To copy a spectrum to be edited into the Spec List from the Library Search window select the spectrum name in the Hit List and use the mouse to drag the selection to the Spec List window Thermo Scientific Creating and Searching Libraries User Guide 53 4 Searching Libraries Setting Li
74. gram and spectrum by default b Choose View Spectrum c Choose Grid gt Delete gt All Cells to remove the chromatogram d Select View and clear all entries except Spectrum to expand the chromatogram to the full size of the Qual Browser window e To enlarge the window display area click in the upper right corner of the window Figure 9 Qual Browser window showing the Chromatogram view of the raw file M Qual Browser steroids14 steroids14 raw File Edit View Display Grid Actions Tools Window Help 8x sjej a Belo DIRAE Bl FHA EEEE eE EE eE e z Q C xcalibur examples data steroids 14 2 28 1996 12 15 58 PM RT 0 00 3 78 a 0 67 NL 100 2 34E6 MCF MS 90 steroids14 80 70 60 50 Relative Abundance 40 30 20 0 09 0 38 047 0 0 05 0 15 2 0 25 3 0 35 Time min NUM 2 Open cells to display the raw data in a grid of four cells as shown in Figure 10 a To display two cells in the window choose Grid gt Insert Cells gt Left b To display four cells in the window choose Grid gt Insert Cells gt Below 16 Creating and Searching Libraries User Guide Thermo Scientific 2 Adding a Spectrum to a Library Viewing a Spectrum in Qual Browser Figure 10 shows the following views clockwise from lower left Scan Filter view filtered Chromatogram view averaged Spectrum view and unfiltered Chromatogram view Figure 10 Qual Browser window
75. hat exported by Qual Browser E Spectra created with the Edit or New buttons in the User Library Manager window M Spectra from the NIST EPA NIH Main library R Spectra from the NIST EPA NIH Replicates library U Spectra from a user library To submit a Spec List spectrum to a Library Browser search 1 Set the Library Search options See Customizing a Search on page 50 2 Double click the spectrum name The Browser displays all search results in the search results Hit List pane see below Comparing a Spec List Spectrum in the Compare Pane To transfer a Spec List entry to the Compare window double click the entry See Displaying Spectra in the Compare Window on page 10 Using the Hit List The Hit List displays a list of library spectra that match the unknown spectrum from highest to lowest match in the Library Search window Each search result is listed with its order number forward and reverse matching factors and a library identifier e M for the Main NIST library e R for the Replicates library e U fora user library Click a name from the search results to display its spectrum and structure in the Plot pane and to display text describing the hit in the Text pane The spectrum also appears in the Compare window 6 Creating and Searching Libraries User Guide Thermo Scientific 1 Overview of Library Browser Library Browser Windows The Plot and Text Panes The Plot panes display the following e
76. he scope of the subtract background file operation e To subtract the entire background file from the input file select the Subtract Whole File option e To subtract a single scan from the background file from each scan of the input file select the Subtract Single Scan RT option and type the retention time for the scan in the associated box Specify alignment and scaling e To offset the subtraction of the background file from the input file type the required offset in the Alignment Offset RT box e To scale the subtraction of the background file from the input file type the required factor in the Scaling Factor box To specify the location of the output file type the full path location for the output file in the Folder box or click the Folder button and browse to the required location The dialog box displays the name of the output file as BG_ lt Input File gt in the Name box To start the subtract background file operation click Process The dialog box closes To abandon the file operation and close the dialog box click Exit Subtracting Background Spectra To subtract background spectra eliminating background peaks from either one range either side of the chromatogram peak of interest or two ranges both sides of the chromatogram peak of interest use the Chromatogram view bd 1 To select two scan ranges for background subtraction To select a spectrum click in the upper right corner of the spec
77. ide Thermo Scientific 4 Searching Libraries Limiting a Library Search 2 Select one or more databases from the available list To use a database constraint select its check box If you do not want to use a database constraint make sure its check box is clear Fine Commercially Available Fine Chemical Index TSCA Toxic Substances Control Act Inventory RTECS Registry of Toxic Effects of Chemical Substances EPA EPA Environmental Monitoring Methods Index USP US Pharmacopoeia U S A N HODOC CRC Handbook of Data of Organic Compounds NIH NIH NCTI Inventory File EINECS European Index of Commercial Chemical Substances IR NIST EPA Gas Phase IR Database The data system only reports search results if they feature in one or more but not necessarily all of the selected databases Applying a Name Fragment Constraint To limit the search to compounds with a specific name or name fragment 1 Select the Enable check box in the Name Fragment area The Name box accepts a text string up to 39 characters to represent a fragment of a compound name for example cyclo The library search filters search results and only returns those containing the specified text in their names The entry is not case sensitive for example CYCLO returns compounds containing the fragments cyclo Cyclo CYCLO and any other case permutations Figure 44 Name fragment area Name fragment Name cyclo 2 Type a name fragment in the Nam
78. ide Thermo Scientific S Y Index A adding a library to the NIST Libraries list 44 adding plots to a view 16 adding spectra to a user library 29 AMDIS 101 append to user library 24 29 attaching a chemical structure to a library entry 32 automated compound identification 101 background subtracting 20 C Compare window 10 compound identification automated 101 constraining a library search 52 57 Constraints tab 52 contacting us ix converting libraries to another format 46 copying a library from the NIST Libraries list 45 CRC Handbook of Data of Organic Compounds database 59 creating a library entry with your spectral data 15 16 43 46 custom reports example 69 deconvolution automated 101 deleting a library from the NIST Libraries list 44 dialog boxes Library Browser ID Number Search 53 Library Search Options 51 Spectrum Information 122 Search Properties for libraries 63 documentation survey ix Thermo Scientific E element constraints 60 elements in compound 61 EPA Environmental Monitoring Methods Index database 59 European Index of Commercial Chemical Substances database 59 exporting spectrum to Library Browser 22 F Fine Chemical Index database 59 H hits list using 6 ID Number Search dialog box 53 L Librarian window 12 libraries adding to NIST Libraries list 44 attaching structures to figure 35 36 converting to another format 46 copying from NIST libraries list 45
79. ientific 4 Searching Libraries Selecting Libraries to Search Selecting Libraries to Search To select a library to search click on the Library Search Options page see Figure 38 on page 54 The Search List page of the Search Properties dialog box opens see Figure 47 This dialog box lists the names and search order of libraries to be used in library search processing The list on the left of the dialog box shows the available libraries The list on the right of the dialog box shows the selected libraries in their search order Figure 47 Search List view Search Properties Search List Search Parameters Available libraries Selected libraries replib lt lt Remove OK Cancel Help The Xcalibur data system generates the Available Libraries list dynamically Each time you open the Search Properties dialog box the current list of libraries available on the system at that time appears This current list might display libraries that do not exist on the system they might have been selected on another system or deleted or renamed since the method was created When you click OK in the Search List view all libraries in the Selected Libraries list are checked If any of them do not exist a warning dialog box opens To include a library in the search list 1 To open the Search Properties dialog box choose from these options From the Qual Browser window choose Actions gt Library gt Options and click the Sea
80. in the Included Libs list and click X e Click the Search tab and observe the Automation check box in the Other Options area Figure 67 Ifthe check box is checked for Automation go to Step 5b save the parameters and close the Library Search Options dialog box e Ifthe check box is not checked go to Step 5a to set automation options 82 Creating and Searching Libraries User Guide Thermo Scientific Thermo Scientific a b 4 Searching Libraries Searching a Library Using Library Browser To set automation options for searches click the Automation tab and select the Automatic Search On check box The following figure shows possible settings for the option to automatically search libraries when exporting spectra to Library Browser Figure 69 Automation page Library Search Property Click OK to save your options close the dialog box and return to the Library Browser windows This action sets automatic searching as the default option the next time you open the Library Browser 6 Double click the entry in the Spec List pane to begin a library search The interactive panes of Library Browser change to display the results of the search see Figure 70 Hit List History drop down list shows the results of the search Hit List pane contains a list of spectral results Structures panes tab display the chemical structure of the compound associated with the highlighted entry Text panes display compound name
81. ing Libraries Editing a User Library 3 To copy the search result to the Spec List pane a Select the Hit List entry you just created Right click this entry and select Copy from the shortcut menu b To make the Spec List pane active move the cursor to the Spec List pane and left click the mouse button c To paste the entry to the Spec List window right click to display the shortcut menu and choose Paste 4 Click the Librarian tab The Librarian window opens see Figure 21 Figure 21 Librarian window 3 NIST MS Search 2 0 Librarian Io File Search Yiew Tools Window Help a x LCAL EEA sjaja ofal X i x Sr c Name 1004 ae ad ms hydro A sterai oad 267 505 281 291 150 170 190 210 230 250 270 290 310 330 350 370 ms2test hydrocortisone 2 Name hydrocortisoneM5S2 Formula MW N A CASH N A NIST N A ID 2 DB ms2test Other DBs None Comment F c Full ms2 363 30 40 00 1 50 00 375 00 10 largest peaks 309 999 327964 267505 281450 291 448 249 402 297392 251 380 269314 263311 Synonyms ro synonyms Names A Structures Spec List Plot Text A Plot_ Lib Search Other Search Names Compare Librarian For Help press F1 Thermo Scientific Creating and Searching Libraries User Guide 33 3 Managing Libraries Editing a User Library 5 To save the structure of the entry from the library to the entry a In the Li
82. ing and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Editing a User Library 6 To edit the spectrum information a Display the Librarian window by choosing Window gt Librarian in Library Browser b Select the unedited entry in the Spec List pane as shown in Figure 27 Figure 27 Librarian window showing a spectrum in a list of entries 3 NIST MS Search 2 0 Librarian steroi hydro 129 a 301 331 349 100 120 140 160 180 200 220 240 260 280 300 320 340 30 Text File steroids 4 113 129 RT 1 32 1 47 AV 17 NL 2 33E4 Name steroids 4 1 13 129 RT 1 32 1 47 AV 17 NL 2 33E4 Formuk MW N A CAS N A NIST N A ID 9 DB Text File Other DBs None Comment T c Full ms2 331 30 40 00 100 00 350 00 10 largest peaks 295999 277755 109723 253714 313498 271 405 213399 221387 225375 171375 Synonyms ro synonyms c Click led The Spectrum Information dialog box opens d Select all of the text in the Name box and type a name for the entry e Click Add to Library The Choose Library to Save to dialog box opens f To copy the new spectrum entry to the selected library click OK The entry Text File in the Librarian window does not change Thermo Scientific Creating and Searching Libraries User Guide 39 3 Managing Libraries Editing a User Library 7 To copy and paste the library entry from the Hit List pane to the Spec List pane see Fig
83. is an example report of a library search that you can print from Qual Browser Hit 3l RSI 2 454 651 3 383 523 4 343 34 5 317 491 6 311 336 7 296 303 8 282 32 9 270 337 10 266 555 11 266 266 12 259 306 13 246 432 14 244 329 15 244 378 16 R3 470 17 232 310 18 227 305 19 225 362 20 220 293 21 720 395 22 205 530 23 200 345 24 19 275 25 190 521 26 179 249 27 178 461 28 177 353 29 174 221 30 169 232 Relative Abundance w D pe a pi 53 2 83 8 8 x P U a ng AAAA w a 200 Prob 0 98 0 14 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 NameLibrary Proge MS2TEST DeoxyMS2TEST HydraiNiSTDEMO MethyMS2TEST AldostNISTDEMO CoichNiSTDEMO Folic ANISTDEMO 17a MNISTDEMO HydroWISTDEMO ReserNISTIDEMO DistanNISTDEMO SqualcNiSTDEMO ErgotcNISTDEMO DiethyNISTDEMO SuUlfisoNSTDEMO OctacNiSTDEMO TestosiNISTDEMO WarfaiNiSTDEMO BenzeNISTDEMO 3 MetiNISTDEMO 1 3 CyNISTDEMO Chole NiISTDEMO ChlorcNISTDEMO OctacNSTDEMO BenzeNISTDEMO BenzeNISTDEMO MethcNISTDEMO OctakNISTDEMO TripheiNISTDEMO Hycrocoribonems2 Forua MW O CAS NA Eritry4 7 OH OH 309 397 346 373 309 327 346 373 300 350 steroids 4 51 75 RT 0 59 0 82 AV 25 NL 5 13E4 F c Full ms2 363 30 40 00 150 00 375 00 St 980 RSI 981 MS2TEST Entry 1 CASH NA HycroconisonemS2 Raw data Library entry a 161 181 215 225 249 275 292 305 327 M45 355 Retative Abundan
84. it can show multiple spectra There are three panes in the Compare window The top pane is a plot of the spectral display the middle pane is a standard difference display pane and the bottom pane displays multiple spectra from the Hit List Figure 5 Compare window E Compare Tool 3 spectra to compare 51 2 1216 24 3034 39 43 53 60 65 74 79 86 o 10 20 30 40 50 60 70 80 90 100 110 120 Text File Bergere ritro 9 a Berzere ritro 9 COs iffereree W C Y OUOUOUOUOUO C C S raere rifro Difference A_Headto Tall A Side by Side Subtraction 7 Hit 1 mainib Benzene ritro Hit 2 mainib Berasic acid 2 ritro Hit 3 mainib 2 6 Pyidinedicarboxyic acid The Compare window uses the standard Difference Display options as follows Difference Shows peaks from the first often upper spectrum and second often lower spectrum along with the difference Head to Tail Shows only the two spectra being compared The first spectrum points upward the second spectrum points downward from a common axis Side by Side Shows only the two spectra displayed next to each other Subtraction Creates a spectrum derived by subtracting the second spectrum from the first Displaying Spectra in the Compare Window To add spectra to the top pane 1 Double click an entry in the Spec List of the Library Search window or select an entry in either the Spec List or the Hit List of the Library Search window
85. ive Abundance w 2 we w w wW 2 m z Table of Results RT Scan Probability Name 1 99 164 98 65 MethyltestosteroneMS 2 1 99 164 0 98 HydrocortisoneMS2 1 99 164 0 30 Deox ycorticosteroneMS2 1 99 164 0 00 ProgesteroneMS2 100 120 40 160 0 200 220 240 260 280 300 260 280 SI 790 349 324 275 340 RSI 795 349 325 369 360 CAS NA NA NA NA 96 Creating and Searching Libraries User Guide Thermo Scientific A Library Sample Reports Reports from a Library Search Using Sequence Setup Spectrum of Raw Data steroids 15 261 RT 3 15 P NL 4 4464 T cFul me 315 30 40 00 100 00 320 60 ra 8 F 2 4 kii 2 no 120 wo wo 180 200 220 240 260 280 300 320 340 360 mz Difference Spectra Raweota Library entry Relative Abundance 1720 no 160 0 200 220 240 260 280 300 32C m z Library Spectrum of Most Probable Hit 31 802 RSI 806 MS2TEST Entry 4 CAS NA ProgesteroneMS2 Relative Abundance Table of Results RT Scan Probability Name Si RSI CAS 3 15 261 98 74 ProgesteroneMS2 802 806 NA 3 15 261 0 98 HydrocortisoneMS2 432 434 NA 3 15 261 0 22 DeoxycorticosteroneMS 2 392 488 NA 3 15 261 0 00 MethyltestosteroneMS2 334 377 NA Thermo Scientific Creating and Searching Libraries User Guide 97 A Library Sample Reports Report from a Library Search Using Qual Browser Report from a Library Search Using Qual Browser The following
86. la MW N A CASH N A NIST N A ID 4 DB Text File Other DBs None Comment F c Full ms2 363 30 40 00 1 50 00 375 00 10 largest peaks 309 999 327964 267505 281 450 291 448 249 402 297392 251380 2693146 263311 Synonyms ro synonyms Names A Structures Spec List Plot Text Plot 7 Lib Search Other Search Names Compare Librarian For Help press Ft i 30 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libraries Editing a User Library 2 To display the Spectrum Information Dialog Box box see Figure 19 click el The dialog box opens displaying information specific to the spectrum Figure 19 Spectrum Information dialog box showing raw spectrum information Spectrum Information Name steroids 4 250 284 RT 2 98 3 31 AV 3 r Formula From structure r Other Names Synonyms Comments IF c Full ms2 315 30 40 00 100 00 32 Mol Weight jo ID Number 2 CAS Number jo Peaks 129 Library Text File Add to Library Replace Add to List Attach Struct Clipboard Struct creche No structure Exit Help 3 Give the spectrum a new name a Click and drag the cursor in the Name box to highlight the entire text string b Change the default text string of the spectrum to a more useful name Thermo Scientific Creating and Searching Libraries User Guide 31 3 Managing Libraries Editing a User Library Attaching a Chemical Structure t
87. list with new information If you do not select this option data is added to the top of the compare list No structures puts no structures on the compare window Spectra per page specifies the number of structures from the compare list that are shown below the compare window Thermo Scientific Creating and Searching Libraries User Guide 11 1 Overview of Library Browser Library Browser Windows Librarian Window The Librarian window is the User Library manager for the Library Browser Use it to create User Libraries and to add spectrum files and compound information to them Also use the Librarian window to create save and edit text files save mass spectra and edit compound ID information Figure 7 Librarian window W Librarian Ce4HsNog 10 20 30 40 50 60 70 80 90 100 110 Text Fie Bergene ritro 5 2 A Cortisone Name Bergere ritro 5 Formula C H5NO2 MW N A CAS N A NIST N A ID 6 DB Text File Other DBs None Comment Fromirstrument 5 10 largest peaks 77999 51846 123388 50305 93161 S515 2a 92 3 92 B BI MFI C21 H2805 Plot Text The Librarian window is divided into three panes e A Spec List shows the names of all files under consideration including structure and formula if available e A Plot pane shows the spectrum of a file in the Spec List e A Text pane displays any detailed text on the selected file in the Spec List To delete a spectrum Click x to re
88. ll click Open Thermo Scientific Creating and Searching Libraries User Guide 69 4 Searching Libraries Setting Up to Search Libraries Automatically 6 To apply changes to the Reports view click OK Figure 53 shows the Reports view and a specified Report Template Name Figure 53 Processing Setup window Processing Setup Reports Untitled Int Std Djema S tretet 2 See aos C Xcalibur templates CustLibrS earRept2 Yes Yes Yes Yes None 70 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Setting Up to Search Libraries Automatically 7 Save the processing method a Choose File gt Save As The File Summary Information dialog box opens see Figure 54 Figure 54 File Summary Information dialog box File Summary Information b Type file summary information in the Description box and click OK The Save As dialog box opens Thermo Scientific Creating and Searching Libraries User Guide 71 4 Searching Libraries Setting Up to Search Libraries Automatically c In the Save As dialog box type a name the processing method see Figure 55 Figure 55 Save As dialog box L Lx Se ee em ei drugs pmd 4 testinafilters pmd 4 practiceMS2 pmd 4 steroid plus test pmd steroidsMS2 pmd Processing Methods pmd d To save the method and return to the Reports view click Save 8 To close the Processing Setup wind
89. ly 16 X Xcalibur Library Manager Dialog Box Convert Libraries Page 108 Thermo Scientific Creating and Searching Libraries User Guide Index T 127
90. m creates the following e A copy of the exported spectrum in the Xcalibur Libspecs folder The file is given an msd extension with the same filename as the original data file although this is truncated to eight characters 8 3 filename format e An index file containing details about all exported spectra e The data system places the exported spectrum into the Spec List Spectrum List and the Library Browser immediately searches the selected libraries for matching spectra if you check the Automation option in the Library Search Property dialog box To display the Library Search Property dialog box choose Tools gt Search Options To display the Automation option check box click either the Search tab or the Automation tab See Setting Up to Search Libraries Automatically on page 64 Creating and Searching Libraries User Guide 23 2 Adding a Spectrum to a Library Exporting Spectra from the Xcalibur Data System Exporting Spectra Automatically from the Processing Method The processing method contains the Append to User Library option to automatically export a spectrum directly into a user library If the specified library does not exist the Xcalibur data system creates it When a spectrum is added to a user library it contains the following basic information e The complete mass intensity list e A name formatted as lt filename gt lt scannumber gt RT lt rt gt AV lt av gt NL lt nl gt for example steroids02 1 R
91. m wps portal ts contactus To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help e Fill out a reader survey online at www surveymonkey com s PQM6P62 e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Thermo Scientific Creating and Searching Libraries User Guide ix ee B Overview of Library Browser This chapter gives a brief overview of Library Browser describes how to use data exported from Qual Browser and describes how to build and maintain a user library Contents e Library Browser Process Overview e About Library Browser e Library Browser Windows Use Xcalibur Library Browser to do these tasks e Create spectral libraries including MS MS fragmentation libraries e Use the Library Browser to run automatic post acquisition library searches on MS MS fragmentation spectra e Run searches directly from the Qual Browser in the data system or automatically by batch processing data files in the Sequence Setup window using a qualitative processing method Library Browser Process Overview on page 2 summarizes the steps for creating editing and searching custom libraries and printing reports of the results This chapter also provides information about how to choose a peak detection algorithm for the Xcalibur da
92. ment constraint It is used in conjunction with the Condition list and Value box in the same row within the Individual Element table To enter an element constraint click the box and type the required abbreviation For example to apply carbon as an element constraint type C The data system adds a new row to the table for further entries Condition Enter a condition for an element constraint in this box The Xcalibur data system uses this condition in conjunction with the Condition list and Value box in the same row within the Individual Element table Valid conditions are lt less than gt greater than equals To type an element constraint condition click the box to activate the list Click the down arrow and select the required abbreviation 116 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Table 9 Library Search Constraints Page parameters Sheet 3 of 7 Parameter Value Description Type a numerical value for an element constraint in this box The data system uses this value in conjunction with the Condition list and Value box in the same row within the Individual Element table The value represents the number of atoms of the specified element required by library compounds to satisfy the constraint To type an element constraint value click the box and type the required number the valid range is 0 to 99 Elements Present
93. meters Sheet 4 of 7 Parameter Description Mass Spectral Peak Constraints M Build a profile of ions and ion abundances to be matched against library entries during the search The search algorithm only returns search results matching the specified constraints Mass spectral peak Set specific criteria about the mass spectral peaks required in a library hit Each row in constraints table the table represents an individual mass spectral peak constraint There are four components to each constraint represented by the table columns Type Normal Loss Rank or Maxmass m z In a Normal Rank or Maxmass type constraint use this box to type the m z value of the mass spectral peak to limit In a Loss type constraint use this box to type the value of a neutral loss From In a Normal Loss or Maxmass type constraint type the minimum abundance of the constrained mass spectral peak in this box In a Rank type constraint type the lowest position of the ion in an intensity ordered list of spectral peaks in this box To In a Normal Loss or Maxmass type constraint type the maximum abundance of the constrained mass spectral peak in this box In a Rank type constraint type the highest position of the ion in an intensity ordered list of spectral peaks in this box Row Number Enter a new item in the last unused row in the table indicated with an asterisk Each numbered row represents an item in the table 118 Creating an
94. mo Scientific Qual Browser displays this window in its workspace when you submit a spectrum in a Spectrum View to a library search or when you open a result file containing library search results from qualitative processing The Library Search Results window displays matching library spectra hits in a four pane arrangement Clockwise from the top left the four panes are as follows The Hit List lists the best matches found during the library search Three factors describe the accuracy of the match to your spectrum SI A direct matching factor for the unknown and the library spectrum RSI A reverse search matching factor ignoring any peaks in the unknown that are not in the library spectrum Prob A probability factor based on the differences between adjacent hits in an SI ordered list With the SI and RSI matching factors a perfect match results in a value of 1000 As a general guide 900 or greater is an excellent match 800 900 a good match and 700 800 a fair match A matching factor less than 600 is a poor match Unknown spectra with many peaks tend to yield lower match factors than otherwise similar spectra with fewer peaks Creating and Searching Libraries User Guide 123 C Library Reference Library Search Results Window Molecular Structure Difference Spectrum Comparison The probability factor is a complex parameter based on the SI matching factor and the difference between adjacent matches If a hit has an SI match f
95. move a spectrum and any associated library from the list without saving them anywhere To adda spectrum Click to add the highlighted spectrum on the list to a designated User library To move a spectrum Click to remove the highlighted spectrum from the list and put it into a designated user library To delete a user library Click x to remove an entire user library 12 Creating and Searching Libraries User Guide Thermo Scientific Thermo Scientific 1 Overview of Library Browser Library Browser Windows Click the Add Move and DelLib buttons to open a dialog box listing the available user libraries Select the library required for the command When adding or moving a spectrum type a new user library name if required Figure 8 Chose library to copy to dialog box Choose library to copy to List of libraries Library Statistics Spectra ID The dialog box also features buttons for managing individual library entries Click New to create a new library entry Click Edit to change a current library entry in the Spectrum Information dialog box Creating and Searching Libraries User Guide 13 ee i Adding a Spectrum to a Library To create a library entry with MS or MS MS or MS spectral data use the Qual Browser window The procedure in this section uses steroid data The Xcalibur data system stores the raw data files in the C Xcalibur examples data directory To manually create a library
96. n in Figure 17 to add processed spectra to a specific user library Figure 17 Append to user library area Append to user library MV Enable User library Steroids hd Thresholds Match factor f999 Reverse match factor f999 Probability 3 100 To set matching criteria to avoid duplicate entries 1 Select the Enable check box 2 Either select a user library from the User Library list or type a new library name The drop down list includes all currently active user libraries If you type a new library name the library is created only if a spectrum fails the matching criteria Enter the highest possible values in the Thresholds boxes The failed spectrum is appended to the library 3 Type threshold values for Match Factor Reverse Match Factor and Probability To confirm that all spectra are appended to the library type 999 999 and 100 respectively See Submitting a Spectrum to a Library Search on page 56 for an explanation of these threshold values During processing and after any requested enhancement of a relevant chromatogram peak apex scan the Xcalibur data system submits the spectrum to a library search e Ifthe top hit from a library search exceeds or is equal to any one of the threshold values the data system returns the hit list and the spectrum is not appended to the specified library e Ifthe top hit fails to reach any of the threshold values the data system discards the hit list no sear
97. nal cost along with the NIST Mass Spectral Database since January 1998 AMDIS is included with the Xcalibur software and is also available through the NIST internet site www nist gov srd Dromey R G Stefi M J Reindfleisch T C Duffield A M Extraction of Mass Spectra Free of Background and Neighboring Component Contributions from Gas Chromatography Mass Spectrometry Data Anal Chem 1976 48 9 1368 1375 2 Shackelford W M Cline D M Faas L Kurth G An evaluation of Automated Spectrum Matching for Survey Identification of Wastewater Components by Gas Chromatography Mass Spectrometry Analytica Chim Acta 1983 146 25 27 Thermo Scientific Creating and Searching Libraries User Guide 101 B AMDIS Compound Identification Automated Compound Identification Using AMDIS Automated Compound Identification Using AMDIS AMDIS does the following e Performs an automated search of the NIST library e Displays dual chromatographs e Performs batch analyses e Builds user defined libraries using either user provided GC MS files or the NIST Mass Spectral Database e Provides compound class identification e Tracks results of routine performance runs e Uses a library of mass spectra with or without retention indices to identify compounds in a data file AMDIS has two main windows e Results Window e Confirm Window 102 Creating and Searching Libraries User Guide Thermo Scientific B AMDIS Compound Identification Automate
98. ndix A Appendix B Managing the NIST Libraries 3 cious sats sities datnantann dqcaceates batbittete date 43 Adding aLibraty sesse Lac tab baw iia a satne ea ia a mates OA vt ayel ae Nea 44 Deleting a Library i tseni eidar a a ule Mal oan e a Va 44 Copying Libraty ed soc kes ani al Batwa i R a E A 45 Converting Libraries to Another Format os ave dys ae eek os eS wip wees 46 Searching Libraries 00 cece cece e eect eens 49 Custom Zing a Search cro siuen Shae hae yeaa ees 50 Including a User Library in a Search apt agate wack eit ekeedes 51 Limiting a Library Searchissa onni Epa EEEa ae ea NE 52 Searching a User Library Entry by ID Number 00 53 Setting Library Search Option Parameters cee eed aed dee tee ae 54 Submitting a Spectrum to a Library Search ico35 cons oer a ehr eee take 56 Limiting a Library SeatGh amp fees a 6a deste sith lo dessa ahayela diya bhai actmuyerbloy a 57 Applying a Molecular Weight Constraint 0 00 eee 58 Applying the Other Databases Constraint 0 00 cece eee eee ee 58 Applying a Name Fragment Constraint cess piwlees Mpa a ood eer 59 Applying Element Colisttatnts si occisd ask eg aes ad ee a ake ares 60 Applying Mass Spectral Peak Constraint 0 00 00 e eee ee eee 61 Selecting Libraries to Searching pcan cnrraiistrtin kyti a i aae tata memes 63 Setting Up to Search Libraries Automatically 0 0 eee eee eee 64 Specifying Search Pa
99. o a Library Entry To attach a chemical structure from a list of structures to an entry in a custom library use the following procedure Also use the procedure to attach a structure from a program such as ChemDraw ChemDraw saves drawings of chemical structures in the mol file format Because you cannot attach a structure to a text file set the search parameters in Library Browser so that the name of the compound source changes to a name other than Text File in the Librarian window To attach a structure to an entry and change the source of the entry 1 Export a spectrum to a library following the instructions in Exporting Spectra from the Xcalibur Data System on page 22 2 From the Lib Search window select an entry in the Spec List pane Right click this entry and select Library Search Library Browser finds the entry and copies it to the Hit List pane see Figure 20 Figure 20 Library Search window showing the results of searching a library 3 NIST MS Search 2 0 Ident Presearch Default InLib 2322 100 spectra Ei CES m File Search View Tools Window Help A a x AECL EELEAA Boa Name 1 steroids14 51 72 RT 0 59 0 78 AV 22 SB v e ala Name steroids 4 51 72 RT 0 59 0 78 AV 225B 29 A Formuka T MW N A CAS N A NIST H N A ID 5 DB Text File Other DBs None Comment F e Full ms2 363 30 40 00 150 00 3754 10 largest peaks 309
100. ocessing of the selected samples click OK If the data system displays a Save your changes box as shown in Figure 61 click Yes Figure 61 Message box Do you wish to save your changes before reprocessing This sequence has changed it is recommended that you save your changes before reprocessing to keep the sequence in step with the results file 7 To display the Processing Status window see Figure 62 click the Queue Manager task in your computer task bar Figure 62 Processing Status window amp steroids14 Processing ioj x Queue Analysis View GoTo Help uj 8 Oxe Status Run sample reports steroids14 01 51 04 Reprocessing Waiting steroids15 01 51 04 Reprocessing NUM 6 4 99 1 51PM 7 Two beeps signal the end of the batch processing 8 Check your printed reports to see that they provide the information you wanted 76 Creating and Searching Libraries User Guide Thermo Scientific Initiating a Library Search from Qual Browser 4 Searching Libraries Initiating a Library Search from Qual Browser To perform a library search from the Qual Browser window 1 Click aie on the Xcalibur Home Page to display the Qual Browser window 2 To open a raw file that contains steroids data choose File gt Open or click Z in the toolbar The Open Raw File dialog box opens 3 Browse to a raw file and click Open 4 View a spectrum For procedure details see Viewing a Spectrum in Qual Browse
101. og box opens see Figure 66 Figure 66 Print dialog box r Print What Print How O Al One Page Eno C Selected cell only Each cell on a separate page Help 8 Select options for your print display 9 To close the dialog box and preview the results click OK 10 To display the Print dialog box again click Print and click OK 11 Click OK in the second Print dialog box to print the results See Library Sample Reports on page 87 for an example of library search results initiated from Qual Browser 12 Click XJ to close the Library Search Results view Searching a Library Using Library Browser To search a library use the Library Browser window To perform a library search on a spectrum exported from Qual Browser 1 Click in the Spectrum view upper right in the Qual Browser window to activate the window 2 Right click the Spectrum view to display the shortcut menu Note To display data files in Library Browser export them from Qual Browser You can export a spectrum into Library Browser from Qual Browser after opening a raw file raw or a result file rst in Qual Browser 3 Choose Library gt Export to Library Browser to open the Library Browser windows automatically When you export a spectrum to Library Browser the data system automatically does the following e Copies information about the exported spectrum into the C Xcalibur Libspecs directory The data system
102. ome of the options on the Library Search Constraints page these are all normally not active For example you can exclude certain high intensity ions that appear in many compounds or that are present in the spectrum background You can target a search to a particular range of molecular weights or to compounds containing certain elements Using Library Search Constraints requires specific knowledge about the target compounds in the chromatogram This knowledge is not always possible in automated processing The Library Search Constraints page see Figure 41 contains five groups of options to constrain the library search To display the Library Search Constraints page from the Qual view of the Processing Setup window select the Library Search Constraints tab See the following sections to set these constraints e Applying a Molecular Weight Constraint Applying the Other Databases Constraint e Applying a Name Fragment Constraint Applying Element Constraints Applying Mass Spectral Peak Constraint Figure 41 Library Search Constraints page from Qual View Identification Spectrum Enhancement Molecular weight Other databases l Enable jz a a ea ea a Name fragment l Enable Thermo Scientific fa S Bestel Library Search Options Library Search Constraints Element constraints l Enable Element Condition Value gt 0 Mass spectral peak constraints l Enable Type m z From To lt New gt 0
103. ormat of a custom report template 1 Click l on the View bar in the Processing Setup window or choose View gt Reports The Reports view appears see Figure 51 Figure 51 Reports view Processing Setup Reports Untitled Int Std Djema S t1 41s perlol 2 eS Se eee es Ves ves Ves None 2 If the Apply Changes dialog box opens read the message and click Yes 68 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Setting Up to Search Libraries Automatically 3 Click the Enable cell in the Sample Reports area When a check box appears select the check box to make Row 1 active see Figure 52 Figure 52 Reports view with Row 1 active Processing Setup Reports Untitled Int Std Djema S t1 41s perlol 2 _ w Yes Yes Yes None 4 Specify the sample brackets in Row 1 a To exclude the bracket for standards from the report click Yes in the Std column and clear the check box b To exclude the bracket for quality control samples click Yes in the QC column and clear the check box c Click Yes in the Other column and clear the check box 5 Specify the name of a Report Template doc in Row 1 a To display the Browse for Sample Report Template dialog box double click the Report Template Name cell b Scroll to select a report template c To select the report template and display the filename in the Report Template Name ce
104. ound Spectra Using the Subtract Background Tool To change the library search list 1 To open the Subtract Background dialog box choose Tools gt Background Subtract from the Qual Browser window Figure 11 Subtract Background dialog box wA Subtract Background Input File C Xcalibur examples data drugn_02 raw Browse Scan filter c SRM ms2 465 30 cid23 00 419 30 421 30 P All detectors Single detector AE X I Negative chromatograhic subtraction results allowed r Background File Browse m Scope Scaling factor fi 000 r Output Name C Xcalibur examples data BG_drugx_02 raw Folder Folder Proceed 2 To select the input file type the pathname of the input file in the File box or click Browse and locate the file using the Open dialog box 3 To choose the detector s identify data from the required detector source using the Single Detector list To use all the detectors recorded in the raw file select the All Detectors check box 4 To choose a scan filter click the Filter arrow to display filter options that are stored in the raw file Then select a filter 5 To select the background file type the pathname of the background file in the File box or click Browse and locate the file using the Open dialog box Thermo Scientific Creating and Searching Libraries User Guide 19 2 Adding a Spectrum to a Library Working with Background Spectra Select t
105. ow and return to the Xcalibur Home Page choose File gt Exit 72 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Setting Up to Search Libraries Automatically Specifying Raw Data Files in Sequence Setup To search libraries and print reports automatically specify the raw files containing the data to process To display the Sequence Setup window and open a sequence list sId 1 To display the Sequence Setup window click ogi on the Xcalibur Home Page 2 To display the Open dialog box choose File gt Open 3 Scroll to select a sequence file and double click to display the list of samples see Figure 56 Figure 56 Sequence Setup window amp steroid sld Open Sequence Setup ioj x File Edit Change Actions View GoTo Help Wama oeae Sle gt HE 5 m Sample Type File Name Sample ID Inst Meth Proc Meth Position Inj Vol Std Bracket steroids02 Sample02 C Xcal eps les data C Xcaliburexample C Xcaliburexamples methods steroid 20 00 Celtics Std Bracket steroids03 Sample03 C X lt calibur examples data C Xcalibur example C Xcalibur examples methods steroid 20 00 standard Std Bracket steroids04 Sample04 C Xcalibur examples data C Xcalibur example C calibur examples methods steroid 20 00 standardl Std Bracket steroids05 Sample05 C Xcalibur examples data C Xcalibur example C Xcalibur examples methods steroid 20 00 Red Sox Unknown sampled Sample08 C Xcalibur exam
106. ow shows the data used in identification in more detail than the Results window does see Figure 73 Figure 73 AMDIS Confirm window 2 AMDIS Chromatogram Component Mode TEST D File Analyze Mode View Library Options Window Help m C NISTO2 AMDIS32 DATASHPATEST DWDATA MS The Confirm window is divided into the Menu Bar Button Bar top Chromatogram top most graphical display Component Profile middle graphical display Component Target Information list middle numeric display and Component Target Mass Spectra bottom graphical display Creating and Searching Libraries User Guide 105 B AMDIS Compound Identification Automated Compound Identification Using AMDIS Table 2 Confirm window areas and their functions and options Area Function options Menu bar File Analyze Mode View Library Options Window Help Toolbar Run Rescale Info arrow images Chromatogram display View the ion chromatograms for each ion Chromatogram profile View the total ion current and the largest mass chromatogram peaks over the region actually used in the deconvolution of the component Component Target View either component or target data Information Component Target View the raw mass spectrum scan and the deconvoluted spectrum at a given retention Mass Spectra display time Once data has been analyzed this display also shows the mass spectra of the component and the library 106 Creating and Searching Libraries U
107. ox You can specify the same number in both From and To boxes In this case the Xcalibur data system discards a library hit unless the designated mass spectral peak is present in exactly the specified abundance or rank in the retrieved spectrum Absolute Relative Specify how the Xcalibur data system applies the From and To parameters in the Mass Spectral Peak Constraints table Select the Absolute option if you want the application to evaluate all table entries as a percentage of the base largest ion in the spectrum Values must be between 0 and 100 For example if you type 10 and 50 in the From and To fields of a Normal type constraint the application discards any search results in which the specified mass spectral peak is not present at an abundance of between 10 and 50 In the case of Normal and Loss type constraints the abundance values can also be Relative Specify how the Xcalibur data system applies the From and To parameters in the Mass Spectral Peak Constraints table Select the Relative option if you want the application to treat the first entry as an absolute Normal or Loss type The application considers subsequent entries in the table relative to the first In the following example library search results must contain the following e Anion at m z 125 with an abundance between 10 and 50 of the base ion e An ion at m z 250 with an intensity between 50 and 999 of the observed intensity of the first ion in the
108. ples data C Xcalibur example C Xcalibur examples methods steroid 20 00 Unknown sampleB Sample09 C Xcalibur examples data C Xcalibur example C Xcalibur examples methods steroid 20 00 Unknown sampleC Samp C Xcalibur examples data C Xcalibur example C calibur examples methods steraid 20 00 Unknown sampleD Samp C Xcalibur examples data C Xcalibur example C Xcaliburexamples methods steroid 20 00 Unknown sampleE Samp C Xcalibur examples data C Xcalibur example C Xcaliburexamples methods steroid 20 00 Std Bracket steroids13 Sampl C Xcalibur examples data C Xcalibur example C Xcalibur examples methods steroid 20 00 Celtics Std Bracket steroids14 Sampl C Xcalibur examples data C Xcalibur example C Xcalibur examples methods steroid 20 00 standard Std Bracket steroids15 Samp C Xcalibur examples data C Xcaliburexample C Xcaliburexamples methods steraid 20 00 standardl Std Bracket steroids16 Samp C Xcalibur examples data C Xcaliburexample C Xcaliburexamples methods steraid 20 00 standardL 0 00 For Help press F1 NUM 6 24 99 2 43 PM WA OU OA wry 4 To exclude samples from the list highlight rows to exclude and choose Edit gt Delete Row The data system displays a message box to confirm the Delete Row command Click Yes see Figure 57 Figure 57 Sequence Setup window after excluding rows K steroid sld Open Sequence Setup ioj x File Edit Change Actions View GoTo H
109. plication changes the icon to to indicate that it is the active cell b Choose View gt Spectrum or click TJ on the toolbar To display or enhance a spectrum choose from these options e With the spectrum cell pinned click the chromatogram at the point of interest a peak apex for example e To view a spectrum averaged across a peak drag the cursor through the chromatogram peak of interest For more information refer to Selecting a One Dimensional Range on a Plot in Chapter 3 of the Xcalibur Qualitative Analysis User Guide e Enhance the spectrum if necessary by using background subtraction For more information on this step see Working with Background Spectra on page 18 Select the search libraries and other search options For more information see Setting Library Search Option Parameters on page 54 To start the library search choose one of these options e Choose Actions gt Library gt Search e Click J on the toolbar e Right click the Spectrum View and select Library gt Search from the context menu Qual Browser displays the results of the library search in a Library Search Results window For more information about this window see Library Search Results Window on page 123 56 Creating and Searching Libraries User Guide Thermo Scientific Limiting a Library Search 4 Searching Libraries Limiting a Library Search For processing efficiency constrain a library search using s
110. r 5 Select one or more libraries to search a Right click the Spectrum view upper right A shortcut menu appears b To display the Search Properties dialog box see Figure 64 choose Library gt Options from the shortcut menu Figure 64 Search Properties dialog box with selected library Search Properties NISTDEMO Deine Botany x cma __ aw Heo c Confirm that any libraries you want to search are listed in the Selected Libraries list d Click OK to save the settings close the dialog box and return to the Qual Browser window 78 Creating and Searching Libraries User Guide Thermo Scientific 4 Searching Libraries Initiating a Library Search from Qual Browser 6 To start the library search right click the Spectrum view upper right From the shortcut menu choose Library gt Search to submit the spectrum to a library search The data system displays library spectra search results that match the spectrum in a four pane Library Search Results view see Figure 65 Figure 65 Library Search Results view cascaded with the Raw Data view Qual Browser steroids14 e x File Edit View Display Grid Actions Tools Window Help sele a 41s Beals alee eee ola S le aE ee ta HydrocortizoneMS2 Formula MW 0 CASH NA Entrytt 1 H n MS2TEST Progesterone 2 MS2TEST Deoxycorticoster MS2TEST Hydrocortisone STDEMO Methyltestosteron S2TEST Aldosterone STDEMO
111. r on page 16 Figure 63 shows four views clockwise from lower left Scan Filter view filtered Chromatogram view averaged Spectrum view and unfiltered Chromatogram view Figure 63 Qual Browser window A Qual Browser steroids14 Raw Data e x File Edit View Display Grid Actions Tools Window Help la x sele al qp Salm eaa Eeee all Cfo ele Allele all RT 0 00 3 78 Relative Abundance 0 0 0 5 1 0 15 2 0 25 3 0 Time min 35 02 28 96 12 15 58 m E 2 34E6 TIC F Full ms2 363 30 40 00 150 00 375 00 MS steroidst4 steroidsl4 Start S 1 End s 323 Start Time 0 00 End Time 3 77 e Full 363 30 40 00 150 Full 331 30 40 00 100 Full 303 30 40 00 100 Full 315 30 40 00 100 ms2 ms2 ms2 ms2 Thermo Scientific 00 375 00 350 00 310 00 320 00 00 00 00 steroids14 51 75 RT 0 59 0 82 AV 25 NL 5 13E4 F c Full ms2 363 30 40 00 150 00 375 00 100 5 J 804 J 804 404 Relative Abundance J 183 4 205 1711 150 RT 0 00 3 78 Relative Abundance 0 38_0 47 0 0 05 200 209 2 225 1 239 2 309 2 3271 267 2 250 miz 300 NL 2 3466 TIC MS steroidst4 2 01 10 20 217 252 3 01 15 2 0 25 3 0 35 Time min NUM Creating and Searching Libraries User Guide 77 4 Searching Libraries Initiating a Library Search from Qual Browse
112. r library use the Qual Browser window This procedure describes exporting spectra to Library Browser using unenhanced spectra For more information see Working with Background Spectra on page 18 and the previous section Attaching a Chemical Structure to a Library Entry on page 32 Apply the procedures from these related sections to unenhanced spectra when possible before you do the procedure in this section To add library entries from Qual Browser to a user library 1 To display the Qual Browser window click i j Qual Browser in the task bar at the bottom of the monitor screen 2 To display an MS MS spectrum of a relevant peak a Click in the Spectrum view upper right cell in Qual Browser to make the cell active b Move the cursor to the Chromatogram view in the lower right cell Click and hold just to the left of the second chromatographic peak c To average the scans you select drag the cursor horizontally across the peak The Xcalibur data system displays the spectrum in the Spectrum view 3 Right click the mass spectrum to display a shortcut menu 4 To export the spectrum choose Library gt Export to Library Browser The data system displays a message box as shown in Figure 26 Figure 26 Export Message box NIST MS Search 2 0 X You can either OVERWRITE Spec List contents or Q it Prepend Cancel 5 To add the entry to the top of the Clipboard window click Prepend 38 Creat
113. rameters in the Qual View 0 000000 ee 65 Specifying Report Options for Library Searches 00 0000000 68 Specifying Raw Data Files in Sequence Setup 6 0 000s eee eees 73 Processing Raw Files and Printing Reports 0 0c cece ee eee eee 75 Initiating a Library Search from Qual Browser 0000 eee eee 77 Searching a Library Using Library Browser 0 e eee eee eee eee 80 Library Sample Reports 0c cece cece eee eee eee eee eee 87 Reports from a Library Search Using Sequence Setup 00005 87 Report from a Library Search Using Qual Browser 00 0000 ee ee 98 Report from a Library Search Using Library Browser 00000 99 AMDIS Compound Identification nunaa 101 AMDIS Oyerview Bisa he or ce scat alas ou can dst ca E A anche T E 101 Automated Compound Identification Using AMDIS 00 102 Results Window s we ona Mo cares ee ee a Oe eae OE BA 103 Confirm Window tose oh s05 5 004 tcp BOO Soteh od We edie rnnr rrur 105 iv Creating and Searching Libraries User Guide Thermo Scientific Thermo Scientific Contents Appendix Library Reference 000 ec ee cece eee eee eee eee eens 107 Library Manager Dialog Box casc 5 dope Deancsbed sae sen eviee errur rnrn 107 Cotivert Libtaties Page cin Wicd Metabo Wii wr Wie Sali p Da aA 108 Manage Libraries Page cccta0 bales oasis tee ahs eRe 110 Library Search
114. rameters page to select the type of library search limit the search by a molecular weight constraint and determine how the results of the search are returned Table 5 Search Parameters page parameters Sheet 1 of 2 Parameter Description Spectrum Search Type Define the type of library search applied to spectra There are two main options Identity and Similarity The difference between the two search types is primarily in the weightings of the spectrum as a function of mass Identity Apply an Identity search algorithm for library matching of spectra A Normal Identity search is the default option Similarity Apply a Similarity search algorithm for library matching of spectra Normal Apply a Normal Identity search algorithm for library matching of spectra This is the default option A Normal Identity search is suited to low quality or unusual spectra The search algorithm uses a standard pre screen search filter Quick Apply a Quick Identity search algorithm for library matching of spectra Use this option when you are sure the spectrum or compound exists in the library The search algorithm uses a fast pre screen search filter Spectrum Search Options Reverse Search Penalize Rare Specify that the Xcalibur data system sorts matching library spectra hits by the Reverse Search Match Factor By default the data system sorts search results by the Forward Match Factor Reduce the match factors of hit compounds present
115. rch List tab e Right click within a Spectrum view select Library gt Options from the shortcut context menu and click the Search List tab e Click Search List on the Library Search Options page see Figure 38 on page 54 2 Select the library name in the Available Libraries list 3 Click Add to add the library to the Selected Libraries list in the final position Thermo Scientific Creating and Searching Libraries User Guide 63 4 Searching Libraries Setting Up to Search Libraries Automatically To change the search order of selected libraries Select the library name in the Selected Libraries list e Click Top to move the library to the top of the list e Click Up to move the library up one position e Click Down to move the library down one position e Click Bottom to move the library to the last position KD To exclude a library from the search list 1 Select the library name in the Selected Libraries list 2 Click Remove to transfer the library to the Available Libraries list 3 Click OK to save the new settings and close the dialog box Setting Up to Search Libraries Automatically 1 To set up method files in the data system that search libraries automatically 1 Use the Xcalibur Processing Setup window to create a processing method file pmd 2 Use the Sequence Setup window to process data files in a sequence list sld with the processing method that you created For more information about setting up s
116. rt a spectrum from Qual Browser or view a spectrum from the Library Browser To create a user library from Qual Browser 1 To start a new user library export a spectrum from Qual Browser For more information about exporting a spectrum see Exporting Spectra from the Xcalibur Data System on page 22 2 Choose Window gt Librarian 3 In the NIST MS Search 2 0 Librarian window see Figure 14 select a spectrum Figure 14 NIST MS Search 2 0 Librarian window 3 NIST MS Search 2 0 Librarian E Io File Search Yiew Tools Window Help a a x AECL EEA sjaja Cal X 8 gt l 1004 a 504 30 56 18 0 amaaan sanaan ppp meyer r 10 20 30 40 50 60 70 80 90 100 110 mainib 2 Pyrraidinone methyt Name 2 Pyroidinone 1 methyt A Formuk C 5H NO 1 MW 99 CAS 872 50 4 NIST 1024 ID 52875 DB mainib Other DBs None 10 largest peaks 99999 44929 42840 984689 28529 41474 15290 43256 27228 39185 Synonyms 1 M Pyrol 2 N Methybe pyrolidinone 3 N Methybe pyroidone 4 N Methytebutyolactam N MethyF2 pyroldinone 6 N MethyF2 pyroidore 7 N Methylpyroldinone 8 N Methylpyroidone 9 NMP Names A Structures Spec List Plot Text A Plot 7 K Lib Search Other Search Names Compare Librarian For Help press F1 4 Click Add in the Librarian window toolbar 26 Creating and Searching Libraries User Guide Thermo Scientific 3 Managing Libr
117. ry message box opens with the following message Are you sure you want to delete the selected NIST library Click Yes The Xcalibur data system removes the library from the list 110 Creating and Searching Libraries User Guide Thermo Scientific C Library Reference Library Search Options Dialog Box Table 4 Manage Libraries page parameters Sheet 2 of 2 Parameter Description Archive Copy a selected library to another directory on your computer or network Select the library that you want to copy to another directory Click Archive The Archive Library dialog box opens The Archive Library dialog box has the following parameters e Parameter e Description e Destination Specify the location for the selected library Use Browse to select a destination for the selected file Click OK The data system makes a copy of the selected NIST library and stores it in the selected directory Library Search Options Dialog Box Use the Library Search Options dialog box to select and order the libraries used during library searching You can also change the way that the search is carried out The Library Search Options dialog box contains these pages e Search Parameters Page e Libraries Page e Automation Page e Limits Page e Library Search Constraints Page Library View Thermo Scientific Creating and Searching Libraries User Guide 111 C Library Reference Library Search Options Dialog Box Search Parameters Page Use the Search Pa
118. s a mass intensity list and a scan filter of the highlighted entry Plot panes display a single mass spectrum of a selected entry Creating and Searching Libraries User Guide 83 4 Searching Libraries Searching a Library Using Library Browser e Compare pane displays the difference between two spectra and presents them in various ways The following figure shows the library search results for a raw spectrum Figure 70 Library Browser default window tA NIST MS Search 2 0 Ident Presearc fault InLib 259 58 spectra Name steroids 4451 69 RT 0 59 0 75 AV 19 NL 6 6 Formula MW N A CAS N A NIST N A ID 11 DB Text Fil Other DBs None Comment F c Full ms2 363 30 40 00 150 00 375 10 largest 309 999 327969 267507 281 449 291 249 407 297389 251 380 269314 263 Synonyms 150 190 230 270 310 350 10 Text File steroids 4451 69 RT 0 59 0 75 AV 19 NL 6 62 Plot Text of Search Spectrum ristde ma ms2test 747 totalspectra 1000900 800 700 600 500 400 300 200 100 0 290 310 330 350 370 hd hydrocorlisoneMis2 Name hydrocortisonemsS2 Formuk MW N A CAS N A NIST N A ID 1 DB ms2test Other DBs None Comment F c Full ms2 363 30 40 00 1 50 00 375 00 10 largest peaks 309 999 327962 267505 291 449 281 44 249 401 297391 251380 2469315 2463312 Synonyms 150 190 230 270 310 350 ne synonyms ms2test hydrocortisonemS2
119. ser 85 in Qual Browser 80 in Sequence Setup 75 probability threshold 29 Processing method exporting a spectrum 24 Processing Setup Qual view Library Search Constraints page 57 Library Search Options page 54 Search List page of Search Properties dialog box 63 Processing Setup window Reports view 68 Q Qual view Library Search Constraints page 57 Library Search Options page 54 qualitative analysis reprocessing data 75 Registry of Toxic Effects Chemical Substances database 59 reports example of custom 69 printing in Library Browser 85 in Qual Browser 80 in Sequence Setup 75 reverse search match factor threshold 29 S search libraries Automation dialog box 83 search results in Library Browser 32 search results using the hit list 6 search customizing 50 Sequence Setup window figure 73 Sequence Setup specifying files 73 Spec List submitting a search from 6 transferring spectrum to Compare pane 6 Spectral Import Options dialog box 83 Spectrum Information dialog box 122 subtracting background spectra 20 survey link ix Thermo Scientific T Text pane information 7 thresholds append to user library option 29 Toxic Substances Control Act Inventory database 59 U US Pharmacopoeia database 59 user libraries appending spectra 29 creating 25 finding Xcalibur data 53 including in a search 51 maintenance 13 selecting 63 V viewing a spectrum in Qual Browser 16 views cursor actions in 16 using interactive
120. ser Guide Thermo Scientific ee i Library Reference The Library function in the Xcalibur data system provides different reference windows whose elements are defined here For information about Library windows see Library Browser Windows on page 4 Contents e Library Manager Dialog Box e Library Search Options Dialog Box e Spectrum Information Dialog Box e Library Search Results Window Library Manager Dialog Box Use the Library Manager dialog box to manage NIST libraries used with the NIST search software and to convert libraries between the ICIS GCQ ITS 40 MassLab NIST and ANDI MS formats Xcalibur Library Manager supports the following conversions oe ICIS GCO ITS 40 MassLab ANDI MS NIST ICIS GCQIITS 40 v v J MassLab y 7 y ANDI MS Y v v NIST Y vf Note The Xcalibur data system does not directly support INCOS LAB BASE or JCAMP library conversions However MassLab data system users have a conversion program to convert from a LAB BASE user library to a MassLab user library In addition a conversion tool exists in ICIS a UNIX system that can convert a LAB BASE user library to a MassLab user library Thermo Scientific Creating and Searching Libraries User Guide 107 C Library Reference Library Manager Dialog Box The Library Manager dialog box has the following pages e Convert Libraries Page e Manage Libraries Page Convert Libraries Page Use the Convert Libraries page to convert on
121. sing or reprocessing the data the results are the same This guide refers to processed data whether the action is processing or reprocessing To process a list of raw files and print library search reports 1 To display the Sequence Setup window click ogi on the Xcalibur Home Page 2 To select the rows in the current sequence to process in Sequence Setup click and hold on the row number in the first row to process and drag the cursor to the bottom row The data system highlights the selected rows 3 Click on the tool bar or choose Actions gt Batch Reprocess The Batch Reprocess Setup dialog box opens Figure 60 Figure 60 Batch Reprocess Setup dialog box Batch Reprocess Setup L Suanutatam xI IF Pe EG zj M a M M M Ej 4 Confirm that the Process Rows box lists all row numbers for example 1 2 If the numbers are missing double click the box and type the row numbers Thermo Scientific Creating and Searching Libraries User Guide 75 4 Searching Libraries Processing Raw Files and Printing Reports 5 Select M any of the following check boxes e Quan Peak Detection amp Integration Calibration Quantitation Qual Peak Detection amp Integration Spectrum Enhancement Library Search e Reports Print Sample Reports Print Summary Reports e Programs e Create Quan Summary Spreadsheet e Advanced Options e Replace Sample Info 6 To initiate batch pr
122. t on the other hand might not exist on the system They might have been selected on another system or deleted or renamed since the processing method was created b To close the dialog box and return to the Processing Setup window click OK 8 To apply changes to the Identification page click OK 9 Specify the name of the library to search a To display search type options click the Library Search Options tab b To display the list of available libraries click Search List see Figure 50 Figure 50 Search List dialog box Search List EG Available libraries Selected libraries NISTDEMO iiss lt lt Remove l e OK Cancel Save s Default Help c To select a library to search highlight the library name in the Available Libraries list and click Add to move the library name to the Selected Libraries list d Click OK to select that library and return to the Qual view of the Processing Setup window Creating and Searching Libraries User Guide 67 4 Searching Libraries Setting Up to Search Libraries Automatically Specifying Report Options for Library Searches To produce and print reports automatically specify report options from the Reports view of the Processing Setup window after specifying library search characteristics Note For more information about creating custom report templates using Microsoft Word refer to the XReport User Guide To display the raw file data in the f
123. t file in the Options area The Options area shown in Figure 40 contains three ways to customize the library search The Reverse Search and Search with MW options are normally not active e To have the Xcalibur data system sort hits by Reverse Match Factor select the Reverse Search check box e To have the Xcalibur data system sort hits by the Forward Match Factor clear the Reverse Search check box 9 To add new spectra to a user library a In the Append to User Library area check box select Enable b From the User Library list select the target user library c Type a threshold value for Match Factor in the Match Factor box d Type a threshold value for Reverse Match Factor in the Reverse Match Factor box e Type a threshold value for Probability in the Probability box 10 To save the new settings and close the dialog box click OK Thermo Scientific Creating and Searching Libraries User Guide 55 4 Searching Libraries Submitting a Spectrum to a Library Search Submitting a Spectrum to a Library Search To submit a spectrum in a Qual Browser spectrum view to a library search To open a Chromatogram view a Click in the cell where you want to open the Chromatogram view The data system changes the icon to to indicate that it is the active cell b Choose View gt Chromatogram or click E on the toolbar To open a Spectrum view a Click in the cell where you want to open the Spectrum view The ap
124. ta system to use when performing library searches Note Throughout this guide the term Library Browser is used synonymously with the term NIST MS Search National Institute of Standards and Technology Mass Spectral Search Program and Library System to refer to the NIST MS Search desktop Thermo Scientific Creating and Searching Libraries User Guide 1 1 Overview of Library Browser Library Browser Process Overview Library Browser Process Overview Figure 1 provides a summary of the steps you perform to create edit and search libraries and to print reports using the Xcalibur data system When using the Library Browser create a custom user library of MS MS or MS spectra one entry at a time To include a spectrum in a library entry display a qualitative raw file data in Qual Browser Then in Qual Browser you can enhance a spectrum by averaging several scans and by subtracting background scans After enhancing the spectrum you can export the spectrum to Library Browser See Adding Spectra to a User Library on page 29 for more information on this process After exporting the spectrum to Library Browser you can edit the spectrum information For example you can change the name of the entry or specify the molecular weight or the CAS Chemical Abstract Service registry number You can even attach a chemical structure to the library entry or select which mass to charge ratios to include See Managing Libraries on page 2
125. time range 4 To display a mass range chromatogram in the upper left cell a Make a cell active by clicking in the upper right corner b Click and hold an entry in the list The data system surrounds the entry with a box and displays a page cursor Thermo Scientific Creating and Searching Libraries User Guide 17 2 Adding a Spectrum to a Library Working with Background Spectra c Drag the page cursor to the upper left cell and release the mouse button The application automatically applies the filter and displays the mass range chromatogram 5 To display an averaged mass spectrum in the upper right cell a Make a cell active by clicking in the upper right corner b Display a mass spectrum by choosing View gt Spectrum c Click and hold in the upper left cell at a position just to the left of the chromatogram peak d Drag the cursor horizontally across the peak and release the mouse button The Xcalibur data system displays a mass spectrum in the upper right cell This spectrum is the average of the scans in the retention time range that you selected For example see the upper right cell in Figure 10 Working with Background Spectra This topic explains how to remove spectra from a display so that only essential spectra are there e Using the Subtract Background Tool e Subtracting Background Spectra 18 Creating and Searching Libraries User Guide Thermo Scientific 2 Addinga Spectrum to a Library Working with Backgr
126. tional e A default user library NISTDEMO Thermo Scientific Creating and Searching Libraries User Guide 3 1 Overview of Library Browser Library Browser Windows The NIST libraries give access to An extensive collection of chemical names Chemical Abstracts Service CAS registry numbers Molecular formulas and weights Chemical structures You can create user libraries using spectra Exported from Qual Browser Exported automatically by a processing method From other sources including text files The program permits searches in many different ways Find reference spectra most closely matching a submitted spectrum Locate spectra or compounds having certain specified characteristics for example the abundance of certain peaks Display the mass spectra of selected molecules Library Browser Windows The Library Browser contains five main windows with tabs at the bottom of the window Library Search Window Other Search Window Name Search Window Compare Window Librarian Window A description of each of these windows follows To display a specific window click the appropriate tab at the bottom of the screen 4 Creating and Searching Libraries User Guide Thermo Scientific 1 Overview of Library Browser Library Browser Windows Library Search Window The Library Search window of the Library Browser see Figure 2 features eight panes Spec list A scratch pad for storage of imported spectra and database spectra
127. trum Choose Actions gt Subtract Spectra gt 2 Ranges to display the crosshair cursor labeled Click and hold on a baseline region in the upper left cell that is close to the chromatographic peak of interest Drag the cursor away from the peak of interest and across a few scans that are representative of the first scan range to subtract Release the mouse button to define the first range The label on the cursor changes to 2 Click and hold on a baseline region on the other side of the peak of interest 20 Creating and Searching Libraries User Guide Thermo Scientific Ta 2 Addinga Spectrum to a Library Working with Background Spectra Drag the cursor away from the peak of interest and across a few scans that are representative of the second scan range to subtract see Figure 12 Figure 12 Qual Browser window showing background subtracted scans in the Spectrum view upper right P Qual Browser steroids14 steroids14 raw Fie Edit View Display Grid Actions Tools Window Help lels a elo d eee slope T a eee l EEE ee e x aelel Cixcal ibur examples data steroids14 2 28 1996 12 15 58 PM RT 0 00 4 o D oOo po te a Relative Abundance o a o 6 S posit ti gt n 3 78 3 0 27 0 47 0 5 1 5 Time min 2 0 S steroids14 13 88 RT 0 14 0 97 AV 76 NL 2 88E1 NL F Full ms2 363 30 40 00 150 00 375 00 2 3466 ian TIC F
128. ure 28 Figure 28 Library Browser panes showing the results of a search from the Spec List panel 3 NIST MS Search 2 0 Ident Presearch Default InLib 2322 11 spectra Name steroids 4 113 129 RT 1 32 1 47 AV 17 NL Formula MW N A CAS N A NISTH N A ID 9 DB Text File Other DBs None Comment T c Full ms2 331 30 40 00 100 00 350 10 largest peaks 295999 277755 109723 253714 313 271 405 213399 221387 225375 171 Synonyms 100 150 200 250 300 350 nosynonyms Text File steroids 4 1 13 129 RT 1 32 1 47 AV 17 NL 2 Ims2test 11 totalspectra 10 213 225 1000 900 800 700 600 500 40 121 131 145 157 17 185195 deoxycorticosteronreMsS2 Name deoxycorticosteroneM52 Formia MW AA CASH N A NISTH N A ID 10 DB ms2test Other DBs None Comment T c Full ms2 331 30 40 00 100 00 350 00 10 largest peaks 295999 277755 109723 253714 313 496 271 405 213399 221 387 225375 171 37 Synonyms 100 150 200 250 300 350 ne synonyms ms2test deoxycorticosteroneM 52 Plot Text of Hit Pee e PFs 233 a In Library Browser choose Window gt Lib Search to display the Library Search window b Select a file in the Spec List pane Right click this entry and choose Library Search If Library Browser finds the entry the application copies it to the Hit List pane c Select the search results entry from the Hit List Right
129. ware C NIST02 MSSEARCH When you select ICIS GCQ ITS 40 or MassLab as the target library type the Title field becomes active e Type the title for the converted library in this field 3 Make the following choices in the Options area if desired e Select either the Create Replace option or the Append option Create Replace is selected by default When you select NIST as the source library type the Include Replicate Entries from the NIST Library in the Target Library check box becomes active e Click this check box to copy replicate entries When you select the Include Replicate Entries check box the Replicate Library field is active The default replicate library is C NIST02 MSSEARCH REPLIB e To use a different replicate library type the path to the desired library in the Replicate Library field or click Browse to open the Browse for Folder dialog box and find a folder 4 To begin the conversion process click Convert The Conversion Status box displays sequential chronological top to bottom messages such as Started the conversion on SEP 3 1999 at 10 01 please wait Finished the conversion on SEP 3 1999 at 10 02 Converted 570 entries 5 If you have no more tasks to complete with the Library Manager click Exit to close the Xcalibur Library Manager dialog box Thermo Scientific Creating and Searching Libraries User Guide 47 ee Searching Libraries After you create a custom library of spectra you can search
130. y Browser 2 Creating and Searching Libraries User Guide Thermo Scientific 1 Overview of Library Browser About Library Browser Figure 1 Library Browser process overview Create a Library Spectrum Export spectrum to Library Browser Open a raw file in Gual Biows r Display a spectrum gt Create a Library or Add to an Existing Library Specify ent j AP eth ii bike sa a Attach a structure Append other spectra Library Browser library optional iuran Search Libraries and Print Reports Automatically using raw or rst files Specify search parameters in y Specify sequence in y Batch process Processing Setup Sequence Setup choose to print reports Manually using a single spectrum Specify library options Print report search Open a raw file in Qual Browser and Export a spectrum to y Specify library options gt Print reports display the spectrum Library Browser search About Library Browser The Xcalibur data system uses the NIST National Institute of Standards and Technology Mass Spectral Search Program and Library System This system contains up to three different libraries The 2000 version of the NIST EPA NIH Mass Spectral Library containing over 147000 compounds optional e The NIST EPA NIH Mass Spectral Selected Replicates Library of 27750 spectra op

Xcalibur 2.1–2.3 Creating and Searching Libraries User Guide

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