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User Manual Lipid identification using the

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1. e Oldja h 4000 Q Trap mass spectrometer amp Sc Name L Waters QTOF Premier L Thermo LTQ PC 34 1 M H L SHIMADZU LCMS IT TOF M H L Bruker Esquire ion trap mass spectrometer ESI MS MS L L Name 4000 Q Trap mass spectrometer M NH4 MW MW 874108 6 DB Spec List Comment NH4 Prec m z S largest peaks 577 5 999 00 601 5 999 00 575 5 600 00 874 Synonyms Agilent lon Trap SL 4000 Q Trap mass spectrometer 4 Names Structures Spec List idblastbeta neg lipidblastbeta pos 115841 total spectra 630 700 770 840 Spec List 4000 Q Trap mass e MNH Plot Text of Search Sp arch Spec 577 5 601 5 1 x 97 TG 52 3 M NH4 TG 16 0 18 1 1 2 ee pos 444 097 713 TG 52 3 M NH4 TG 16 0 16 0 2 570 600 630 660 630 720 750 780 6840 870 3 lipidblasibeta pos 119 364 022 584 TG 52 3 M NH4 TG 16 0 16 1 2 I4 4000 mass spectrometer Head to Tal 368 332 v TG 52 3 MANAA TGITGU T8 4 lipidblastbeta pos 119 364 022 584 TG 52 3 4 TG 16 0 18 0 1 Head to Tail 368 392R 97 7P 5 lipidblastbeta pos 119 364 022 584 TG 52 3 IM NH4 TG 16 1 18 0 1 Name TG 52 3 M NH4 e TG 16 0 18 1 18 2 lipidblastbeta pos 119 354 0 22 584 TG 52 3 M NH4 TG 17 0 17 1 1 Mw 874 108 69910 DB lipidblastbeta pos 7 lipidblastbeta pos 111
2. io ESI MS MS 447 4 150 00 Aglent lon Trap SL IM Naje Synonyms 4000 Q Trap mass spectrometer M NH4 no synonyms 360 480 500 720 Spec List Bruker Esqure ion mass Lis MGDG 383 M H GDG 18 4 9E 38 9 M H 606 20 5 52 I MGDG 38 9 M H 606 20 5 52 PG 38 5 M H GPGro 18 0 20 5 5z Name MGDG 38 9 06 18 4 62 92 12215 PG 38 5 M H 6 20 5 52 82 1 MW 795 108 8492 DB lipidblasibeta neg Comment Parent 795 50478 Mz exact 795 50478 2 largest peaks pater fi M 301 21662 333 00 ee EE sni 301 21662 999 00 sn2 FA 360 480 600 720 MGDG 38 9 MH MGDG 184 23 Example 5 Name Agilent lon Trap SL M Na PC 18 1 16 0 3SNIST MS Search 2 0 Peptide Presearch Default 136 spectra Search Tools Options Window Heb 218 xi Agilent Ion Trap St Monar O aE Name Agilent lon Trap SL M Na MW 782108 5 DB Spec List Comment PC 18 1 16 0 LC MS Analysis p 723 3 999 001 599 4 900 001 577 5 70 001 478 651 3 10 001 Synonyms e QTOF Premier Thermo LTO PC 34 1 M H SHIMADZU LCMS IT TOF M H Bruker Esquire ion trap mass spectrometer ESI MS MS M H 4000 Q Trap mass epectiometier M NH4 490 560 630 700 Spec List Agilent lon Trap
3. Experimental MS MS list M el 732 555 Da dta MW IDs 7803 DB Text File Comment CHARGE 1 PEPMASS 732 554687 10 lar ks 673 3751991201706 999 00 478 37586510016934 185 76 714 5033631 673 3751991201706 exp MS MS 100 672 382010 496 3987288063696 263 m z Values and Intensities 213 14963098738727 8 26 270 37082386 319 19541630653885 6 65 337 2953131 480 540 Text File 732 555 Da dta 600 4354771383574 NAI 3641ng850f5 b 100 673 100 exp MS MS 476 496 713 ol 426 ___ 460 510 527 549 585 613 531 658 686 1000 900 800 700 600 500 400 300 200 100 0 in silico MS MS 1 32 1 M H 1 476 494 2 pc 855 855 250 0 PC 32 1 GPCho 1 100 B 3 pc 855 855 250 0 PC 32 1 GPCho 1 4 pc 855 855 250 0 32 1 M H GPCho 1 440 460 480 500 520 540 560 580 600 620 640 660 680 700 720 740 5 pc 106 106 000 0 PC 32 1 M H GPCho 2 a 732 555 Da dta Head to Tail MF 438 RMF 901 YPC 321 M H GPCho 16 1 3 6 pe 106 106 000 0 32 1 M H GPCho 8 X Difference Head to Tail Side by Side Subtraction 855 855R 25 0P 7 pc 75 75 000 0 PC 321 GPCho 1 Name PC OPCRO TO TGIZVT6 0 8 pc 75 4 M H GPCho 1 673 48083 i i ds 100 MW 732 ID 3924 DB pc pos h 9 pc 69 A IM H GPChoQ 7 miz Values and Intensiti 10 pc 69 1 IM H GPCho 6 476
4. C Trans Proteomic Pipeline software page http tools proteomecenter org wiki index php title Formats mZXML How can perform quantification of lipid species The LipidBlast library is a mass spectral library for identification of lipids In order to quantify lipids other commonly available vendor software tools must be used This includes the use of internal or external standards reference compounds the use of proper calibration and peak integration methods programs for alignment of LC MS direct infusion MS data For a collection of programs see http fiehnlab ucdavis edu staff kind Metabolomics LipidAnalysis For alignment programs see peak alignment of LC GC MS NMR data http fiehnlab ucdavis edu staff kind Metabolomics Peak Alignment Or see our poster using the Genedata Refiner MS program An automated workflow for rapid alignment and identification of lipid biomarkers obtained from chip based direct infusion nanoelectrospray tandem mass spectrometry http fiehnlab ucdavis edu staff kind Metabolomics LipidAnalysis lipids biomarker workflow pdf Which lipid classes are covered the LipidBlast libraries Currently the glycerophospholipids are available in NIST MS MSP format Other libraries monoacylglycerols diacylglycerols and triacylglycerols and galactolipids MGDG DGDG SQDG are also available Additional libraries can be developed on request or by using the provided data templates The creation of i
5. GPCho 10 0 22 5 4Z 7 Z 10Z 13Z 16Z 44 746 500 Da 745 5 1 LipidBlast pos 38734 746 D 1 746 57 117 156 5 7 672 PC 33 1 GPCho 15 0 17 1 92 44 745 500 Da 746 5 2 LipidBlast pos 38739 746 D 1 745 57 117 156 5 7 672 PC 33 1 M H GPCho 17 1 8Z 15 0 44 746 500 Da 745 5 3 LipidBlast pos 38724 746 D 1 74657 113 151 48 670 PC 33 1 GPCho 15 0 18 1 11E 45 748 500 Da 748 5 1LipidBlast pos 43937 748 0 748 49 271 343 930 PC 32 4 GPCho 8 0 24 4 5Z 87 117 147 45 748 500 Da 748 5 2 LipidBlast pos 43954 748 0 748 49 271 343 6 6 930 PC 32 4 GPCho 24 4 5Z 8Z 11Z 142 8 0 45 748 500 Da 748 5 3 LipidBlast pos 43944 748 0 748 49 270 342 6 4 917 PC 32 4 GPCho 14 1 92 18 3 BZ 97 122 46 750 500 Da 750 5 47 754 500 Da 754 5 1 LipidBlast pos 44046 754 0 754 54 423 625 3 7 974 PC 32 1 16 0 16 1 72 47 754 500 Da 754 5 2 LipidBlast pos 44047 754 0 754 54 423 625 3 7 974 PC 32 1 GPCho 16 0 16 1 92 47 754 500 Da 754 5 3 LipidBlast pos 44048 754 754 54 423 525 3 7 974 PC 32 1 M Na GPCho 16 1 72 16 0 48 756 500 Da 756 5 1 LipidBlast pos 44079 756 0 756 55 400 640 21 4 987 PC 32 0 GPCho 16 0 16 0 48 756 500 Da 756 5 2 LipidBlast pos 44077 756 0 756 55 370 611 6 961 PC 32 0 M Na GPCho 14 0 18 0 48 756 500 Da 756 5 3 LipidBlast pos 44081 756 0 756 55 370 611 6 961 PC 32 0 GPCho 18 0 14 0 49 758 50 Da 758
6. 31425 600 00 M H sn2 H20 11 pc 61 6 7000 32 1 IM H GPCho 1 6 31425 478 32989 600 00 M H sn1 H20 12 pc 51 51 0 00 0 32 1 IM H GPCho 1 50 549 48829 494 32481 600 00 M H sn2 13 pc 54 54 0 00 0 PC 32 1 M H GPCho 2 496 34045 600 00 M H sn1 14 pp 54 54 000 0 PC 32 1 M H GPCho 549 48829 400 00 M H C5SH14NO4P 183 0 4 M H GPChoQ 673 48083 999 00 M H C3H9N 59 0 1 M H GPCho 2 v 480 540 600 660 720 714 54377 400 00 M H H2O 18 Compare Librarian Hit List pc pos h 32 1 M H GPCho 1 6 1 92 16 0 Plot Text of Hit L in silico MS MS Peptide 2 Figure NIST MS search GUI with the LipidBlast libraries loaded Library Search Options Search Libraries Automation Limits Constraints Humber of Hits ta Print Include Spectrum Plot in Report Draw Structure in Plots Apply Maximum Spectrum Length 2000 Return Focus to Caller upon Completion Automatic Search Automation of library search is obtained by starting nistms exe with the par 4 option from the DOS command prompt which writes all results into NISTLOG txt in the same directory The option nistms exe par 8 stops the automated result logging The automation options are set in the library options dialog The number of hits is the most important selection Library search options and m z tolerances The NIST MS Search option MS MS search has to be sele
7. 347 016 714 TG 52 3 M NH4 TG 16 1718 1 1 Comment Parent 874 78589 Mz_exact 874 78589 8 lipidblasibeta pos 11 347 016 714 TG 52 3 M NH4 TG 17 1717 171 4 largest peaks 9 lipidblasibelapos 85 284 005 585 TG 52 3 M NH4 TG 17 0 17 2 1 575 50362 333 001 577 51926 399 001 601 5192t 4 m z Values and Intensities 575 50362 999 00 M NH4 sn2 18 577 51926 999 00 M NH4 sn3 18 857 78315 601 51926 999 00 M NH4 sn1 18 857 78315 199 80 M NH4 17 630 700 770 840 24 How does the text based format look like The library is natively stored in NIST MSP text format That allows an easy conversion to all possible machine specific or program specific formats Name PC 36 4 M H GPCho 20 4 7E 10E 13E 16E 16 0 MW 782 56995 PRECURSORMZ 782 56995 Comment Parent 782 56995 Mz_exact 782 56995 36 4 M H GPCho 20 4 7E 10E 13E 16E 16 0 C44H80NO8P Num Peaks 7 764 55939 400 M H H20 18 723 49645 999 M H C3HON 59 599 50391 400 M H C5H14NO4P 183 544 34043 600 M H sn2 526 32987 600 M H sn2 H20 496 34043 600 M H sn1 478 32987 600 M H sn1 H20 Due to the standardized format the library is versatile and universal applicable Fragments are annotated as accurate masses and specific fragments are named In silico MS MS experimental MS MS K7823L 408 58 AV 1 NL 3 18E1 Name 32 1 M
8. 4 2010 4 03 PM B My Docuimenke DLipidBlastBeta pos File Folder 6 4 2010 4 03 PM p My Computer E 55220757 HLM 1KB HLM File 6 4 2010 6 44 PM B 3 314 Floppy A 64220757 HLM 1KB HLMFile 6 4 2010 6 44 PM LWC C 5 ABI Danaher 4000 Q Trap Ex 1KB Windows Installer P 12 10 2009 3 48 PM E Aailent iontrap Example PCp 1KB Windows Installer P 12 10 2009 3 48 PM E OQ AutoImp MSD 1KB MSD File 6 4 2010 2 13 PM jS Bruker Esquire Iontrap MGD i 1KB Windows Installer P 12 10 2009 3 47 PM B ctNT66 dll 240 Application Extension 8 14 1998 12 03 PM 5 InpMzxml dll 116 KB Application Extension 11 5 2009 8 15 F E E Library his 1KB HISFile 6 4 2010 4 04 PM i5 msichi dll 44 KB Application Extension 10 22 2009 2 34 PM 16 LipidBlastBeta MSSearch 5 nistcmn dll 496 KB Application Extension 10 22 2009 2 34 PM E LipidBlastBeta neg NISTMS20 WRN 1KB WRN File 6 4 2010 6 30 PM C3 LipidBlastBeta pos a nistms32 dll 500 KB Application Extension 5 5 2010 3 04 PM nistms exe 40KB Application 7 18 2008 11 14 AM F NISTMS chm 176 KB Compiled HTML Help 1 26 2010 11 01 AM Jnistms exe 1 636 KB Application 12 3 2009 2 07 PM F nistms INI 14 KB Configuration Settings 6 4 2010 4 04 PM F E NISTMS SPL 7KB Shockwave Flash 6 4 2010 4 04 PM 5 nistrekn dll 224 KB Application Extension 10 22 2009 2 33 PM Other his HIS File 6 4 2010 4 04 PM a ri dl
9. PC 34 1 GPCho 16 0 1 PC 34 1 GPCho 18 1 1 34 1 M Na GPCho 18 1 1 34 1 M Na GPCho 18 1 1 PC 34 1 M Na GPCho 18 1 1 480 50 640 720 Name PCs Pos ID CE45 014165 218 RT 0 33 1 0 Mw N A 9 DB Text File Comment T IT ITMS p ESI d Full ms2 782 50 cid45 EEI 599 548 001 577 67 00 467 1 722 8001 478 7001 441 6001 664 Text File PCs_Pos_ID_ 018165 218 RT 0 3 4 of Search Sj _ 1 PC 34 1 M Na GPCho 18 1 4l v P tipidblastbeta pos P PC 341 GPCho 16 0 480 560 640 720 21 8 largest peaks 723 49409 999 00 599 50155 600 00 441 2 518 32243 20 001 526 32751 20 00 544 3 Single search examples for ABI Agilent Bruker Thermo Waters Example 1 Name Waters QTOF Premier M H PE 17 0 17 0 tA NIST MS Search 2 0 Peptide Presearch Default 1 spectrum Bie Search Tools Options Window laixi ATT lt d 11 waters QTOF Premier tn amp amp amp N L Waters QTOF Premier M H L Thermo LTQ PC 34 1 L SHIMADZU LCMS IT TOF M H L Bruker Esquire ion trap mass spectrometer ESI MS MS M H L L Name Waters Premier M H Mw 718 108 1 DB Spec List Comment PE 17 0 17 0 Prec m z 718 4834 5 largest peaks 269 2297 999 00 718 4834 800 00 719 1092 5t Synonyms Agilent
10. SL Plot Text of Search Sp Search idblastbeta neg lipidblastbeta pos 115841 total spectra Tm 2 ii 4 593 PC 34 1 M Na GPCho 10 0 2 3 lpidblasibelapos 593 917 235 949 PC 34 1 M Na GPCho 12 0 2 4 Ipidblastbetapos 593 917 235 949 PC 34 1 M Na GPCho 14 0 2 5 lipidblastbetapos 593 917 235 949 PC 34 1 M Na GPCho 14 0 2 Name PC 34 1 M Na GPCho 8 07261092 6 lpidblasibetapos 593 917 235 949 PC 34 1 M Na GPCho 14 0 2 MW 782108 42014 DB lipidblastbeta pos 7 lipidblastbetapos 593 917 235 949 PC 34 1 M Na GPCho 14 0 2 Comment Perent 782 96759 Mz_exact 782 5575 8 lipidblastbetapos 593 917 235 343 PC 34 1 M Na GPCho 14 1 amp 9 ipidbasbelapos 5929 917 235 998 341 GPCho 15 1 S i med Sa o 638 45253 ETE 10 lipidblastbeta pos 593 917 2 35 349 PC 34 1 GPCho 16 0 1 m z Val 11 lipidblastbeta pos 593 917 235 949 PC 24 1 M Na GPCho 16 0 1 CERERI M Na 59 sn2 12 lipidblastbeta pos 593 917 235 949 PC 24 1 GPCho 16 0 1 38818675 2000 M Na sn2 H20 13 ipidblasbeapos 593 917 235 949 PC 34 1 GPCho 16 0 1 656 46319 AM em v 14 lipidblastbeta pos 593 917 2 35 943 PC 34 1 GPCho 16 0 1 w 5933 50155 600 00 M Na C5H14ND4P 183 SNIST MS Search 2 0 Peptide Presearch Default 9 spectra File Search View Tools Options Window Help 8
11. sn2 H20 12 lipidblastbeta pos 855 941 552 984 PC 341 M H GPCho 18 1 1 496 34043 600 00 2 13 lipidblastbeta pos 856 941 552 984 PC 34 1 M H GPChe 18 1 17 ES ret nl H20 lipidblastbeta pos 984 PC 34 1 M H GPCho 18 1 4E w 260 390 520 650 577 51960 400 00 M H C5H14NO4P 183 lipidblastbeta pos 34 1 GPCho 16 0 1 24 Plot Text of Hit 22 Example 3 Name SHIMADZU LCMS IT TOF SQDG 34 3 ANIST MS Search 2 0 Peptide Presearch Default 4 spectra Name icon ot M H Walere QTOF Premier M H Mw List Themo PC 34 1 MoH comen ESTER Prec m z 815 499 S gem meng er MS MS M H 999 001 553 258 600 001 255 003 300 0 Agilent lon Trap SL synonyms 4000 Q Trap mass spectrometer 4 250 380 520 650 Spec List SHIMADZU L LCMSAT TOF HE TTET 2 MH SQDG 16 0 18 006 34 3 MH SQDG 18 3 amp z 3 5006 34 3 MH SQDG 18 3 7 1 POE 537 27348 260 380 520 lipidblastbeta ug UE 34 3 Hk SQDG 16 0 1 Example 4 Name Bruker Esquire ion trap mass spectrometer ESI MS MS M H MGDG 38 9 NIST MS Search 2 0 Peptide Presearch Default 6 spectra Name Bruker Esquire tap n mass spectrometer ESI QTOF Premier Thermo LTQ PC 34 1 M H comment 000 20 5 18 4 MGDG 38 3 M H Pre tr Pt EE 2755 450 001 537 5 400 001 795
12. the automatic start of the NIST MS Search GUI Please refer to http chemdata nist gov for DLL integration and all technical question 3 Use of MGF compiled dta file This method is used by Hundreds of proteomics groups and supported by all major mass spectrometry vendors NIST MS GUI can read MGF files Please use Google to find out more http Awww google com num 100 amp hl en amp safe active amp q MGFt and DTA files 26
13. 0 MS2 precursor 788 50 PCs Pos ID CE45 01344165 218 RT 0 33 1 02 AV 2 NL 2 42E3 MS2 precursor 790 50 T Average spectrum MS2 782 50 165 218 MS2 precursor 732 50 100 MS2 precursor 796 50 MS2 precursor 798 50 MS2 precursor 804 50 MS2 precursor 806 50 MS2 precursor 808 50 MS2 precursor 810 50 E MS2 precursor 812 50 MS2 precursor 814 50 MS2 precursor 818 50 MS2 precursor 820 50 J MS2 precursor 824 50 1 MS2 precursor 826 50 MS2 precursor 832 50 250 300 350 400 460 500 550 600 650 700 750 Time min 723 45 Relative Abundance 388 888828 338 36 369 36 441 18 467 27 526 45 608 64 657 55 719 55 764 45 o NM 4 20 Right click with mouse in Xcalibur PCs Pos ID CE45 01 165 218 RT 0 33 1 02 AV 2 NL 2 42E3 T Average spectrum MS2 782 50 165 218 100 Relative Abundance 90 80 70 60 50 40 30 20 10 ns Options 508 64 657 55 719 55 Double click spectrum 1 positive ID with 3NIST MS Search 2 0 Peptide Presearch Default 136 spectra Thermo LTO PC 34 1 M H e SHIMADZU LCMS IT TOF M H Bruker Esquire ion trap mass spectrometer ESI MS MS Agilent eh SL 34 1 GPChof16 0 1 PC 34 1 M Na GPChof16 0 1 34 1 GPCho 16 0 1 PC 34 1 M Na GPCho 15 0 1 34 1 M Na GPCho 16 0 1 34 1 GPCho 15 0 1
14. 5 1 LipidBlast pos 44090 758 0 758 47 322 479 23 8 943 33 6 11 0 22 6 47 77107137167 197 Detailed technical information Installation of the LipidBlast libraries using a Virtual Machine Technical Recommendations The LipidBlast libraries require the installation of multiple software programs In order to comply with industry computer safety standards and for testing purposes it is recommended to install all programs into a Virtual Machine Some of the programs are not compatible with older Microsoft NET dot net technology so all required updates must be installed Visit Virtual machine Wikipedia the free encyclopedia to learn more about Virtual Machines For ease of use we use the freely Microsoft Virtual PC and install a licensed purchase required operating system or test license from Microsoft for Windows XP Windows Vista or Windows Server Universities can obtain a research license for VMWare Workstation or a free Sun Virtual Box license Free Sun Virtual BOX www virtualbox org Free Microsoft Virtual PC 2007 Microsoft Virtual PC 2007 OS Downloads Microsoft Windows Server 2003 R2 Enterprise Edition VHD Windows Server 2008 Evaluation Virtual Hard Drive Images ZIP files 7Zip program for UNZIP operations of packed files zip gz Follow the recommendations and install the Microsoft Virtual PC 2007 and install any licensed Windows XP Windows Vista or Windows Server operating system into the virt
15. H GPCho 16 1 92 16 0 T ITMS Full m amp 8Q 732 58 cid30 00 190 00 745 00 MW 732 55433 476 48 PRECURSORMZ 732 55433 1005 Num Peaks 7 952 714 54377 400 M H H20 18 673 48083 999 59 90 549 48829 400 M H C5H14NO4P 183 e 496 34045 600 M H sn1 478 32989 600 M H sn1 H20 80 494 32481 600 M H sn2 476 31425 600 M H sn2 H20 m 704 Name PC 32 1 M H GPCho 17 0 15 1 9Z J TM MW 732 55433 65 PRECURSORWMZ 732 55433 602 Num Peaks 7 j 714 54377 400 M H H20 18 g 357 673 48083 999 M H C3H9N 59 8 549 48829 400 M H C5H14NO4P 183 9 J 480 30917 600 M H sn1 45 462 29861 600 M H sn1 H20 2 as 510 35609 600 M H sn2 492 34553 600 M H sn2 H20 35 Name PC 32 1 M H GPCho 17 1 9Z 15 0 30 MW 732 55433 25 PRECURSORWMZ 732 55433 672 07 Num Peaks 7 20 591 51 714 54377 400 M H H20 18 153 EL dS 695 39 724 61 673 48083 999 M H C3HON 59 630 28 670 40 549 48829 400 M H C5H14NO4P 183 103 534 25 i 482 32481 600 M H sn1 49638 549 58903 623 82 464 31428600 INH 420 LL EE Ld 508 34045 600 M H sn2 0 CITED TTL EET TPE ET EOD TRL PET TOE En FTT EFETTETET FEES TFETEETTTEE RT EET EFFET TTE TE TEE TT 490 32989 600 M H sn2 H20 150 500 550 650 700 Z Figure The in silico fragment left match the experimental MS MS spectra
16. IST MS Peptide search This batch file uses DeconMSn exe as MGF file creator create cluster mfg bat automatic processing of Thermo raw files e This Windows batch files automates the whole process of a creating dta files b clustering similar spectra c rewriting the clustered m z precursor ions e creating the mgf file which can be imported into NIST MS Peptide search This batch file uses extract msn exe as DTA file creator and MGF files must be created independently or by MSCluster Visual 2008 Redistributable Package x86 e Required for C applications can be downloaded from Microsoft vcredist x86 exe i5 Nomenclature changes for glycerophospholipids Please be aware that the nomenclature changed so now the short term abbreviations are used in all LipidBlast libraries with the long version in the explanation For current updates see online LipidMaps Updates http www lipidmaps org data classification classification updates html Table Changes in nomenclature Previous New GPCho PC GPEtn PE GPSer PS GPGro PG GPGroP PGP GPins PI GPInsP PIP GPInsP2 PIP2 GPInsP3 PIP3 GPA PA GPP PPA CL CL GCDP CDP DG glycan GP glycan GP glycan GP ns glycan PI GPnCho PnC GPnEtn PnE 16 How was the LipidBlast library created The fragmentations were obtained from the literature and LipidMaps data and validated using external reference compounds standards Those reference compounds were inves
17. SSearch Download here http peptide nist gov software ms pep search gui MSPepSearch html pen Remove selected Input MGF Mascot generic or MSP NIST 5 ZCluster ok mgf File Folder Select Sout MS MS libraries to search Select Remove selected Z LipidBlast neg Z NLipidBlast pos Reset to defaults Dutput directory path ptions Presearch mode m z limits Fast Standard Min fi 2000 1 infinity M Search tolerance settings Precursor ion tolerance m z units o4 Ignore peaks around precursor Fragment peak m z tolerance 04 Include precursor m z in the output Min match factor MF to output 0 399 fi 00 Include Hit Unknown precursor m z difference Min peak intensity 1 399 mm Output the input spectrum number Calculate rev dot Max number of output hits Use number of replicates Q TOF Show spectra without matches Set program priority above normal Load libraries in memory Done _ Define precursor and product ion accuracy select number of output hits do not load into memory current bug that prevents libraries searched and press run An tsv file with library search scores will be created which can be imported into EXCEL or OpenOffice Calc Num Unknown Precursor m z Rank Libra 19 Rev Dot Peptide 38 734 566 Da 734 555 3 Lip
18. User Manual Metabolomics Fiehn Lab Lipid identification using the LipidBlast libraries 100 673 Experimental MS MS spectrum 50 476 496 715 549 613 426 451 pi Boy 585 604 658 686 549 715 50 476 494 In silico MS MS spectrum 1 7 673 ZN 440 460 480 500 520 540 560 580 600 620 640 660 680 700 720 740 a 732 555 Head to Tail 436 RMF 901 32 1 MAF GPCho 16 1 9 Tobias Kind and Oliver Fiehn Fiehnlab November 2012 v46 Contact Dr Tobias Kind http fiehnlab ucdavis edu staff kind General Disclaimer The following information is provided for research purposes only and may contain errors LipidBlast Introduction What is LipidBlast LipidBlast is a collection of in silico electrospray tandem mass spectral libraries for the identification of neutral and polar lipid species In the current development stage around 120 000 MS MS spectra covering multiple glycerophospholipid classes and possible ESI adducts are included For more resources regarding lipids and analytical techniques please visit e LipidMaps e Lipid Analysis with GC MS LC MS FT MS Metabolomics Fiehn Lab The LipidBlast libraries were developed from known theoretical fragmentations and experimental fragmentation and abundance information from tandem mass spectra MS MS The experimental basis was a Thermo Finnigan LTQ linear iontrap instrument equipped with an Advion Nanomate nanoESI robotic infusion system However the lib
19. chnology Copyright 2008 by the U S Secretary of Commerce an behalf af the United States of America All Rights Reserved Portions copyright 1984 1996 Corporation F airCom and c tree Plus trademarks of Faicom Corporation and are registered in the United States and other counties All Rights Reserved NIST MSPepSearch for high throughput annotation e Software for batch interpretation of tandem mass spectra Especially useful for thousands of tandem mass spectra evaluations can be around 1500 spectra second http peptide nist gov software ms pep search gui MSPepSearch html Sashimi file conversion utilities e Tools for conversion of MS MS spectra to mzXML and subsequent dta and mgf conversion can be found at http proteowizard sourceforge net and http sashimi sourceforge net MS Clustering e The clustering tool is required to improve signal to noise ratio from infusion mass spectra Similar MS MS spectra are clustered according to selected precursor accuracy and a single consensus spectrum is created Mscluster exe accepts several formats among them dta mgf mzXML For LC MS data a retention time tolerance match may be required or true mass spectral deconvolution because peak data at different retention times should not be clustered MSCluster can be downloaded from http peptide ucsd edu or http proteomics ucsd edu Software MSClustering html 14 Thermo extract msn exe for dta fil
20. cted as seen in the picture An MS MS search precursor mass tolerance of 0 001 Da or in case of accurate mass data and 0 4 m z units for unit mass spectrometers should be selected The product ion mass can be less stringent due to hydrogen shifts 0 4 to 0 8 Da is acceptable Library Search Options XI Options X Search MS MS Libraries Automation Limits Constraints Search MS MS Libraries Automation Limits Constraints Spectrum Search Type identiti Similarity Pogoro Precursor lan m z in spectrum Other Options Automation MS MS Search m z Tolerance Precursor 04 Product tons 04 Spectrum Search Options Reverse Search Penalize rare compounds Ignore Precursor Peptide MS MS Options Auto Report Apply Limits Use Constraints Presearch Defaut Fast Off Structure Similarity Search Options Match Number of Rings Cancel Help Peptide Options Cysteine modification Mone m Score Threshold mw Display qr lo E Omesa log lib 099 Reverse Impure Scoring Omesa Replicates Prob only Otot coed Figure MS MS search and appropriate m z windows must be selected MS MS options are selected using reverse search and low score thresholds all other options are off Library selection an
21. ctrometer ESI MS MS M H 577 407 346 84 522 283 193 91 700 322 180 9 5 L Agilent lon Trap SL Synonyms 5 L 4000 Q Trap mass spectrometer M NH4 no synonyms 283 044 260 380 520 650 Spec List Thermo LTQ PC 34 1 gt Plot Text of Search Sp Search Spect A Plot Text of Spec Ust 7 idblastbeta neg lipidblastbeta pos 115841 total spectra 577 407 1 281 012 336 295 401 088 1 a PC 341 M H GPCho 16 0 18 2 rere pos m E 384 PC 341 IM H GPCho 16 0 18 3 lipidblastbeta pos 855 941 552 984 PC 341 GPCho 16 0 18 4 lipidblasibetapos 866 941 552 984 PC 34 1 M H GPCho 16 0 18 Head to Tail 866 3418 5 52P 5 lipidblastbeta pos 866 341 5 52 384 PC 34 1 GPCho 15 0 18 Name 34 1 M H GPCho 16 0 18 1 11E 6 lipidblastbeta pos 866 941 552 984 PC 34 1 M H GPCho 16 0 18 701 51214 Mw 760108 36547 DB lipidblastbeta pos 7 lipidblastbeta pos 856 941 552 984 PC 341 M H GPCho 16 0 18 Comment Parert 760 58564 Mz_exact 760 5856 8 lipidblastbetapos 866 941 552 984 PC 341 M H GPChof16 0 18 2 largest peaks 9 lipidblastbeta pos 865 941 552 984 PC 34 1 M H GPCho 16 0 18 r r 74257508 20000 455 34 10 lipidblastbeta pos 866 341 5 52 384 PC 34 1 GPCho 18 1 111 7 m z Val Int 11 lipidblastbeta pos 855 941 552 984 PC 341 M H GPCho 18 1 11 478 32992 600 00 M H
22. d Currently M H M Na M NH4 for both positive and negative ESI are covered Special iontrap fragmentations not mentioned in the literature before are also covered Intensities can be modeled according to iontrap or QTOF data and different CID ionization potentials The current libraries are developed using 25V CID as reference for peak abundance modeling Sub exportMSMSZmspPCi Program for converting MS MS fragmentation data into MSP files for NIST Peptide search written by Tobias Kind 2009 fiehnlab ucdavis edu License CC by Creative commons by attribution commercial and non commercial use allowed Dim PrintString String Dim extMSPName String Dim MSPNameString String Start with GlobalMassMin itself CLasSChange ALL For i 1 To 5476 Step 1 Name KKEEEELVALE 3 PrintString Name amp Range X amp 6 1 amp amp amp Print FileNumUrite PrintString MU 1317 PrintString MW amp RoundFixed Range AC amp 6 ij Rounding iccuracy Print fFileNumWrite PrintString PRECURSORMZ PrintString PRECURSORMZ amp RoundFixed Range AC amp 6 i Roundinc Print FileNumWUrite PrintString Comments put all in for copy paste PrintString Comments amp Range X amp 6 i amp amp M H amp Print FileNumUrite PrintString Figure Around 2000 lines of EXCEL VBA code were used for MSP export 17 Auto
23. d install options The libraries must be activated and visible in the right window If no library is selected make sure to edit the install directory NISTMS ini or simply delete the NISTMS ini file and restart nistms exe The program will create a new INI file and will ask for the current library directory Library Search Options Search MS MS Libraries Automation Limits Constraints Available Libs Included Libs lipidblastbeta neg lipidblastbeta pos lipidblastbeta neg lipidblastbeta pos gt gt Add gt gt 115841 Spectra in 2 Libraries 115841 Spectra in 2 Libraries 5 m search Cancel Help Installation NIST MS Search LipidBlast procedure step by step The install assumes a fully patched Windows OS Vista XP Server Extract the directories from the zip file and place it under C for instant use or install into any subdirectory of your choice requires selection of library path The folder should be C LipidBlastBeta MSSearch Start nistms exe to work with the program fit C LipidBlastBeta MSSearch File Edit View Favorites Tools Help sack e M 2 Search 2 Folders Address C C LipidBlastBeta M5Search 1 The NIST MS Search GUI Folders x Name Size Date Modified B Desktop us LipidBlastBeta neg File Folder 6
24. e extraction e This tool is part of Thermo Xcalibur 2 0 and used for extraction of dta files from data dependent scans and for the creation of mgf files combined dta files A license must be obtained from Thermo Fisher Inc DeconMsSn optional tool for dta and mgf extraction e 5 is a tool for dta and mgf file extraction from PNNL It requires the installation of the Thermo XCalibur software and multiple Microsoft dot NET upgrades DeconMSn can be downloaded at http omics pnl gov DTASuperCharge optional tool for dta and mgf extraction e DTASuperCharge is a GUI driven tool for file creation and can be obtained from the following server http msquant sourceforge net mgfprecursor exe tool for precursor ion annotation e After the clustering algorithm spectra contain only cluster IDs For the NIST MS Peptide Search it is more convenient to have attached m z precursor values That also allows better evaluation during automation issues The tool requires the MS Virtual V2008 redistributable package installed as well as all Microsoft dot NET updates The tool is provided as source in C for Visual and also as executable create clustererd mgf bat automatic processing of Thermo raw files e This Windows batch files automates the whole process of a creating dta files b clustering similar spectra c rewriting the clustered m z precursor ions e creating the mgf file which can be imported into N
25. gment names and modeled abundances The following mass spectral search modes can be applied A Traditional mass spectral library search B MS MS database search The LipidBlast libraries can be used with traditional library search procedures such as PBM search or dot product NIST MS search Better performance and better hit rates and higher identification rates are obtained if the accurate precursor mass is included for pre filtering possible lipid species and a subsequent MS MS peak matching is performed The NIST MS Search algorithm is capable of finding a single mass spectrum in a library of one million spectra in only milliseconds How can extract MS MS spectra If your platform software has MS MS search capabilities just import the provided ASCII MSP spectra into your vendor software If your platform has no MS MS search capability which includes precursor search and product ion search step not to be confused with normal mass spectral library search you can extract MS MS spectra export them as MFG files MASCOT format and import them directly into NIST MS Search or NIST MSPepSearch These approaches are used in the proteomics community since many years so talking to a fellow proteomics researcher will solve that problem A For extraction of MGF directly from raw files download ProteoWizard http proteowizard sourceforge net B Other software can be found at the Sashimi tools http sourceforge net projects sashimi files
26. idBlast pos 43806 734 D 1 734 47 274 342 1 5 953 PC 31 4 GPCho 8 0 22 4 7 Z 10Z 13Z 16Z 38 734 523 Da 734 523 1 LipidBlast pos 43807 734 0 15 73447 331 468 10 1 949 31 4 GPCho 11 0 20 4 BE 11 14 39 734 623 Da 734 523 2 LipidBlast pos 43808 734 0 15 73447 331 468 10 1 949 PC 31 4 GPCho 11 0 20 4 5Z 87 117 147 39 734 623 Da 734 523 3 LipidBlast pos 43809 734 0 15 73447 331 468 10 1 949 31 4 GPCho 11 0 20 4 7 E 13 16 40 736 500 Da 736 5 1 LipidBlast pos 38614 736 D 736 49 160 187 50 653 PC 33 6 GPCho 11 0 22 5 4Z 7 Z 10Z 13Z 16Z 19Z 40 736 500 Da 736 5 2 LipidBlast pos 38615 736 0 736 49 160 187 50 653 PC 33 5 GPCho 2Z B 4Z 7 Z 10Z 13Z 15Z 192 11 0 41 735 500 Da 736 5 42 742 500 Da 742 5 1 LipidBlast pos 43904 742 74254 345 508 6 2 948 PC 31 0 M Na GPCho 6 0 25 0 42 742 500 Da 742 5 2 LipidBlast pos 43923 742 0 742 54 345 508 6 2 948 PC 31 0 GPCho 25 0 6 0 42 742 500 Da 742 5 3 LipidBlast pos 43903 742 0 74254 334 496 4 2 947 PC 31 0 M Na GPCho 5 0 26 0 43 746 500 Da 746 5 1 LipidBlast pos 43929 746 0 746 47 289 404 11 931 PC 32 5 GPCho 12 0 20 5 5Z 8Z 11Z 14Z 17Z 43 746 500 Da 746 5 2 LipidBlast pos 43934 746 0 74647 289 404 11 931 PC 32 5 GPCho 20 5 5Z 82 112 142 172 12 0 43 745 500 Da 746 5 3 LipidBlast pos 43927 746 0 746 47 279 392 7 8 919 PC 32 5
27. l 120KB Application Extension 12 3 2009 1 15 PM jl shimadzu LIT TOF SQDGneg s 1KB Windows Installer P 3 17 2010 2 52 PM BA exe 212KB Application 10 22 2009 4 39 PM jl Thermo LTQ PCpos msp 2KB Windows Instaler P 6 4 2010 2 56 PM Te ver2 Man pdf 637 KB Adobe Acrobat Doc 7 25 2008 11 22 AM fl waters QTOF Premier Examp 1KB Windows Installer P 1 27 2010 8 02 PM is 2161 91 59 Application Extension 7 20 2005 11 48 D The NIST MS Search GUI is a freely available program developed by the Mass Spectral Data group at NIST The current distribution of the ZIP file contains a working version of the NIST MS Search GUI program See http chemdata nist gov and the NIST help file Ver20Man pdf for further information 2 The LipidBlast libraries The LipidBlast libraries are developed by Tobias Kind Kwang Hyeon Liu Do Yup Lee and Oliver Fiehn Fiehnlab June 2010 v31 http fiehnlab ucdavis edu staff kind 1 and 2 are independent developments and not associated with each other 10 Using LipidBlast high throughput mode LipidBlast can be used to annotate lipids from large MS MS files with the NIST MSPepSearch The search speed is several hundred spectra per second and thousands of spectra can be annotated at once 1 Import the MGF file on the top window 2 Select an output drive 4 Select the LipidBlast directories from the prior GUI installation such as C LipidBlastBeta M
28. lon Trap SL 4000 Q Trap mass spectrometer M NH4 466 2518 Names Structures Spec List 330 440 550 660 jastbeta neg lipidblastbeta pos 115841 total spectra Spec List Waters QTOF Premier 34 0 GPEtn 17 0 17 0 320 remier Head to Tail 360 400 440 480 520 560 540 Name PE 34 0 GPEtn 17 0 17 0 W 718108 17854 DB lipidblastbeta neg Comment Parents718 53869 Mz_exact 718 53869 I 3 latgest peaks 269 24790 999 00 466 29353 200 00 448 2829 3 m z Values and Intensities 269 24790 999 00 snl FA sn2 FA 448 28297 50 00 M H sn1 H20 Il M H sn2 H20 466 29353 200 00 M H sn1 II M H sn2 zz 466 29353 330 440 550 660 lipidblastbeta neg 34 0 GPEtn 17 0 17 1 Plot Text of Hit Example 2 Name Thermo PC 34 1 M H PC 34 1 SiNIST MS Search 2 0 Peptide Presearch Default 118 spectra Ble search Tools Options Window la x mae 1 Thermo LTQ 34 1 M H 1 tol amp amp Thermo 34 1 M H Mw IDH 2 DB Spec List 1 Waters QTOF Premier M H 2 L Thermo LTQ PC 341 M Hje ne PEPMASS 760 61 IEEE M H e Prec 3 L SHIMADZU LCMS IT TOF 701 314 393 001 504 335 808 51 496 299 576 8 4 L Bruker Esquire ion trap mass spe
29. mated generation of clustered MGF files for Thermo XCalibur The install assumes a clean totally patched 32 bit Windows OS Vista XP Server The current procedure describes the extraction of MS MS data as dta files Please refer to the Internets for more information about DTA MGF PKL files Those formats are very common in the proteomics community and there exist many web resources The clustered MGF files are important because they will be imported into the NIST MS Search program MGF files usually contain multiple MS MS scans The current procedure describes the installation for Thermo Finnigan XCalibur RAW format For other vendors please refer to web or vendor information 1 Install XCalibur 2 0 with all service packs 2 Create a directory CAMSMS Create a directory CAMSMS work Create a directory C MSMS MSCluster Copy create cluster mfg bat into the work directory Copy mgfprecursor exe into the work directory The files UnifiedFile dll Fregistry dll and Fileio dll are part of XCalibur and are needed in the directory unless no PATH is set Copy extract msn exe from the XCalibur install into the CAMSMS work directory Copy PCs Pos ID CE45 01 raw as example file into the CAMSMS work directory When using DeconMSn exe XMGF the MGF file is directly created by DeconMSn In this case please use create clustererd mgf bat Otherwise the file have to be bundled into an DTA file independently In case of problems open the BATCH file Copy c
30. n silico libraries depends on the correct molecular species enumeration and existence of molecular structures and secondly on a correct nomenclature to help during the discovery process Secondly experimental spectra from reference standards must be obtained for all possible classes all possible side chain modifications That includes symmetric sn1 and sn2 side chains different degrees of unsaturation and different head groups Table LipidBlast lipids and current adduct libraries including lyso forms for some species Short Positivemode Negative mode Glycerophosphoethanolamines PE MeH M Na MH Glycerophosphoserines ps ws Glycerophosphoglyceros lowabundan M H _ Glycerophosphoinositos PI lowabundant MH Sphingomyeiins SM MeH MeNa lowabundan DDeggyers pao menna merima TAG MeNH5MeHGMNNa Sufoquinovosydiaoylgyceros SQDG duda Hu HR monomannoside Diacylated phosphatidylinositol Ac2PIM2 dimannoside Triacylated phosphatidylinositol Ac3PIM2 MH dimannoside Tetraacylated phosphatidylinositol 4 2 dimannoside Sulfatides Some of the adducts may not occur in the literature because ions may be suppressed in mixtures but ions were observed from authentic standards Also common adducts such as M Li may not be included because e
31. n the folder CAMSMS work needs to be deleted so only the current raw file will be processed Multiple raw files can be processed together Congratulations You created a combined and clustered MGF file with multiple MS MS scans 19 Automated transfer for Thermo XCalibur users Special section for Thermo XCalibur users for LC MS and Infusion MS data MS MS spectra are automatically transferred to NIST MS GUI XCalibur currently does not transfer accurate product ion masses only accurate precursor masses that works in principle with every software via the locator file autoimp msd and an invoked start of nistms exe Start XCalibur goto MS MS Qual Browser PCs Pos ID CE45 O01 raw Ele Edt Display Grid Actions Tools Window Help 1 slez S lel 510191 eve e m jeje d AOpteron Savet APCs Pos ID CE45 01 11 7 2008 10 41 38 AM 54 x Time range min 0 00 1 61 Tr Mass range Mass tolerance 0 50 Normalize composite spectrum J MS2 precursor 758 50 J MS2 precursor 760 50 J MS2 precursor 762 50 MS2 precursor 772 50 W MS2 precursor 774 50 MS2 precursor 776 50 MS2 precursor 778 50 3 MS2 precursor 782 50 RT 0 00 1 61 dA 9 71E6 TIC MS PCs Pos 1 b CE45 0 Relative Abundance 1 28 0 0 0 2 0 6 os 1 0 1 2 1 4 16 Average spectrum MS2 782 50 MS2 precursor 784 50 MS2 precursor 786 5
32. raries are platform independent and can be used for all MS MS or MS platforms from all mass spectrometry vendors including ABI Sciex Agilent Bruker Shimadzu Thermo Waters and others 100 673 Experimental MS MS spectrum 50 476 496 715 549 613 426 451 511 527 585 604 658 686 549 715 50 476 494 In silico MS MS spectrum 1 2 673 440 460 480 500 520 540 560 580 600 620 640 660 680 700 720 740 a 732 555 Da dta Head to Tail MF 438 RMF 901 YPC 32 1 MAF GPCho T6 1 9 Figure LipidBlast libraries showing an experimental MS MS spectrum and a matching computer generated in silico mass spectrum with similar fragment peaks and abundances How can the LipidBlast libraries be used The LipidBlast can be used for identification of polar lipids using high resolution and low resolution tandem mass spectrometer data In any case the precursor mass is needed from the MS spectrum and the datadependent MS spectra must be extracted from the experimental runs Therefore the LipidBlast libraries can be used for identification of lipids from A Infusion mass spectrometric experiments with data dependent MS MS scans B LC MS experiments with data dependent MS MS scans C LC MS experiments with TOF MS experiments The LipidBlast libraries are traditional mass spectral libraries One difference to other in silico libraries is that accurate mass information is included for all precursor and product ions as well as fra
33. reate cluster mfg bat which contains a documented structure of all calls which will be executed 3 Download any Windows compatible Perl distribution AtiveState Perl and install it Set it PATH so PERL scripts can be executed in every directory 4 Copy merge pl to the work directory CAMSMS work If DeconMSn exe XMGF is used please adjust all parameters in the BATCH file for MGF file creation including the isolation width and m z tolerance 5 Start mgfprecursor exe if an error message occurs install the Visual 2008 Redistributable Package x86 vcredist x86 exe Microsoft Core XML Services MSXML 6 0 msxml6 msi Microsoft NET Framework Version 2 0 Redistributable Package x86 dotnetfx exe For compiling the source make sure to statically link the MFC in the compiler options 6 Download MSCluster MSCluster 20080609 1 zip extract the ZIP into the folder C MSMS MSCluster Create the directory C MSMS MSCluster in Create the directory C MSMS MSCluster out Create the directory C MSMS MSCluster tmp 18 7 Start the file create cluster mfg bat That will process the example file PCs Pos ID CE45 01 raw and will create the combined MGF file merge ok mgf which will be used in the NIST MS Search GUI The MGF file is created in the folder is directly used for library search Comment The mscluster exe accepts multiple formats dta mgf mzXML Two example batchfiles are provided for msn extract Important The old raw file i
34. right The peak abundances in experimental MS MS spectra may fluctuate or in case of overlapping compounds may differ in some cases from the in silico model 25 want to integrate LipidBlast with my own software program The LipidBlast libraries available under the Creative Commons by attribution CC BY license LipidBlast In silico created MS MS libraries for lipid profiling License CC by Tobias Kind Metabolomics Fiehn Lab 2009 http fiehnlab ucdavis edu staff kind http creativecommons org licenses by 3 0 CC BY means you are free to Share to copy distribute and transmit the work to Remix to adapt the work Under the following conditions Attribution You must attribute the work in the manner specified by the author or licensor but not in any way that suggests that they endorse you or your use of the work There are three easy options 1 Direct Integration Load the MSP files LipidBlastBeta neg msp and LipidBlastBeta pos msp via an internal parser into your vendor specific mass spectral search program Make sure to implement an accurate precursor window search and an additional MS MS matching dot product Add the CC BY license 2 Automatic transfer to NIST MS Search GUI Your program transfers the mass spectral file into NIST MS Search GUI It uses and locator file autoimp msd The accurate mass file with precursor and product ions is transferred to the NIST MS Search GUI and a function call invokes
35. tigated using different ionization voltages and using multiple solvents FOS Meutral Mautral 1 Fragment H20 Fragment C3H9M Fragment C5HTEMCI Short Mam SA acgl los SH1 H20 SH acgl loss 5 2 2 Pre PreCursor H Preiturzor amp PreCurzoar 1 36 4 495 3326 477 3221 5433325 B25 3221 782 5700 764 5594 723 4965 699 5039 0 PC 36 4 AET 3013 443 2308 5713533 B5 3533 Toz orin 764 5594 T23 4855 5353 50 3 354 433 2701 4212535 533 3852 581 3845 782 5700 764 5594 723 4965 699 5039 e 36 3 575 3352 465 2857 47 2762 784 5856 TEE B Th 725 5121 601 5136 3 PC 36 3 545 3483 Bay 4853327 477 3221 754 5956 TESTS 725 5121 601 5196 3 PC 36 3 545 3483 485 3327 221 724 5556 TEE 57h 725 5121 601 5136 2 PC 36 3 547 3533 523 3534 493 3170 475 3065 784 5956 TESTS 725 5121 601 5196 e PC 36 3 547 3539 523 3534 493 3170 475 3065 784 5856 TEE B Th 25 521 601 5136 2 PC 36 3 547 3639 523 3534 493 3170 475 3065 784 5956 TESTS 725 5121 601 5196 e 36 3 547 3533 523 3534 493 3170 475 3065 784 5856 TESTAI 725 5121 601 5136 3 PC 36 3 BT 3170 499 3065 5233538 505 3534 794 5956 TESTS 725 5121 601 5196 Figure The LipidBlast libraries were developed from EXCEL templates containing all highly probable fragmentations In principle every possible electrospray ESI or atmospheric pressure chemical ionization APCI adduct can be modele
36. ual machine Each new virtual environment requires a single OS license unless used under WIN7 Read more in the following publication Software platform virtualization in chemistry research and university teaching Tobias Kind Tim Leamy Julie A Leary and Oliver Fiehn Journal of Cheminformatics 2009 1 18doi 10 1186 1758 2946 1 18 http www jcheminf com content 1 1 18 13 Useful software The LipidBlast libraries can be utilized with multiple software packages and workflows We suggest using the freely available and latest version of the NIST MS Search GUI compiled in May 2010 For technical questions please refer to the PDF Handbook Ver20Man pdf NIST Mass Spectral Search Program Version 2 0f provided by the NIST Mass Spectrometry Data Center NIST MS Search GUI at http chemdata nist gov x The NIST Mass Spectral Search Program for the NIST EPA MIH Mass Spectral Library Version 2 0 f build Dec 3 2009 Software by 5 Stein Y Miroakhin D Tchekhovskor and G Mallard Data Evaluation by Mikala J Little Dama hu E White and D Sparkman NIST uses its best effort to deliver high quality copy of the database and to ensure that the data shown are accurate However NIST makes no warranties to that effect and HIST shall nat be liable for any damage that may result from errors or omissions in the database Distributed by the Standard Reference Data Program of the National Institute of Standards and Te
37. xperimental spectra were not acquired and in silico spectra were not modeled yet How large is each single adduct library The size depends on the lipid species but is usually around 5 500 in silico MS MS spectra In case of sphingomyelins the library size is smaller So at the current development stage around 212 516 MS MS spectra from 119 200 structures are included In case of TAGs the library size was reduced to the 2640 most common compounds TG 12 0 12 0 16 0 to TG 22 6 22 6 22 6 due to the large number of combinations NIST MS Search program for easy identification The NIST MS Search GUI is a freely available program developed by the Mass Spectral Data group at NIST The procedure of lipid identification can be easily performed by loading the result mgf file into the NIST MS GUI search By clicking spectrum a library search is performed the green GO button or each single experimental MS MS Hit scores are provided in the left result window See http chemdata nist gov and the NIST help file Ver20Man pdf for further information SNIST MS Search 2 0 Peptide Presearch Default 42 spectra Search Tools Options Window Name 758 571 Da dta 33 759 573 Da dta 34 760 586 Da dta 35 762 599 Da dta 766 536 Da dta 768 555 Da dta pc pos h 5476 total spectra E 1 fi 732 555 Da dta a

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