Welcome! Mass Spectrometry meets Cheminformatics WCMC Metabolomics Course 2014 Tobias Kind. Course: Search of MS/MS files with the NIST MS Search GUI

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1 Biology Informatics Chemistry Welcome! Mass Spectrometry meets Cheminformatics WCMC Metabolomics Course 2014 Tobias Kind Course: Search of MS/MS files with the NIST MS Search GUI CC-BY License 1

2 General workflow for MS/MS search low resolution Iontrap Triple-Quad Q-TOF 1) Precursor match TOF-TOF Orbitrap MS/MS spectrum 2) Product ion search LipidBlast 200k tandem mass spectra Results with annotation Report with with scores high resolution FT-ICR-MS Instrumentation Data processing LipidBlast DB Lipid identification 1) The precursor filter removes 99% of all false candidates within a given mass window. 2) The product ion match uses traditional similarity scoring of remaining candidates.

3 NIST compatible libraries are simply copied as subdirectories under the MSSEARCH directory

4 NIST MS Search GUI (2.0f 2010) Search parameters NIST MSPepSearch mass spectral library search program Thanks to Dmitrii V. Tchekhovskoi and Stephen E. Stein Mass Spectrometry Data Center; National Institute of Standards and Technology (NIST) Visit or for more information, software, or MS libraries.

5 General Library Search view of NIST MS Search GUI

6 The NIST11 full version has MS/MS tree view

7 The NIST MS/MS tree view offers the compound view with different ionization voltages

8 MS/MS search= Precursor filter + similarity filter precursor ion not visible

9 Similarity match of MS/MS spectrum head to tail view

10 Head to tail different spectra

11 Side by side view of MS/MS spectrum

12 Subtraction view of MS/MS spectrum what are the largest peak differences?

13 Transfer (right click in NIST MS Search) to MS Interpreter for further inspection

14 Simple name search not very powerful

15 Sequential search can find anything

16 177 spectra with name fragment galactosyl

17 Powerful sequential search 177 spectra with name fragment galactosyl AND peak at m/z 264 must be between 80% and 100% of base peak

18 Powerful sequential search: Ten result spectra with modified query

19 Formula search how many formulae in database?

20 LipidBlast platform compatibility Num Platforms Num Platforms 1 ABI 4000 Q Trap 24 JEOL JMS HX110A/110A Tandem MS FAB 2 ABI 4700 MALDI TOF/TOF 25 Kratos MALDI TOF AXIMA CFR 3 ABI 4800 MALDI TOF/TOF 26 SHIMADZU KRATOS MALDI TRAP TOF 4 ABI API 2000 triple quadrupole 27 SHIMADZU LCMS IT TOF 5 ABI QSTAR XL QTOF 28 Thermo Finnigan DecaXP ion trap 6 ABI QTRAP Thermo Finnigan LCQ DECA ion trap 7 ABI Sciex API III QQQ 30 Thermo Finnigan LTQ linear ion trap 8 ABI QSTAR Pulsar Quadrupol TOF 31 Thermo Finnigan TSQ Quantum Triple Quadrupole 9 ABI QSTAR XL Quadrupol TOF 32 Thermo Fisher Exactive Orbitrap 10 Agilent 6410 triple quadrupole MS 33 Thermo Fisher LTQ FT 11 Agilent 6520 Q TOF 34 Thermo LTQ Orbitrap 12 Agilent 6530 QqTOF 35 Thermo LXQ iontrap 13 Agilent Ion Trap SL 36 Thermo Orbitrap Velos ESI 14 Agilent Ion Trap XCT 37 Waters AutoSpec magnetic sector MS 15 Agilent LC/MSD 1100 Ion Trap 38 Waters micro QTOF 16 Agilent MSD 1100 single quadrupole MS 39 Waters Micromass Q TOF Micro 17 Agilent QTOF 40 Waters MicroMass QqQ triple quadrupole 18 Bruker DESI FTICR APEX Q 41 Waters QqQ triple quadropole VG Quattro II 19 Bruker Esquire 3000 ion trap 42 Waters QTOF Premier 20 Bruker Esquire ion trap 43 Waters Synapt HDMS 21 Bruker microtof qq TOF 22 Bruker UltraFlex II MALDI TOF TOF 23 Bruker ultraflextreme MALDI TOF/TOF

21 LipidBlast compound coverage Number positive MS/MS spectra Number negative MS/MS spectra Total MS/MS spectra Total lipid compound number Number MS/MS spectra Number Number LipidClass Short Number compounds with different adducts MS/MS LIBS No neg MS/MS No pos MS/MS 1 Phosphatidylcholines PC Lysophosphatidylcholines lysopc Plasmenylphosphatidylcholines plasmenyl PC Phosphatidylethanolamines PE Lysophosphatidylethanolamines lysope Plasmenylphosphatidylethanolamines plasmenyl PE Phosphatidylserines PS Sphingomyelines SM Phosphatidic acids PA Phosphatidylinositols PI Phosphatidylglycerols PG Cardiolipins CL Ceramide 1 phosphates CerP Sulfatides ST Gangliosides [glycan] Cer Monoacylglycerols MG Diacylglycerols DG Triacylglycerols TG Monogalactosyldiacylglycerols MGDG Digalactosyldiacylglycerols DGDG Sulfoquinovosyldiacylglycerols SQDG Diacylated phosphatidylinositol monomannoside Ac2PIM Diacylated phosphatidylinositol dimannoside Ac2PIM Triacylated phosphatidylinositol dimannoside Ac3PIM Tetraacylated phosphatidylinositol dimannoside Ac4PIM Diphosphorylated hexaacyl Lipid A LipidA PP Total All libraries

22 Example Thermo LTQ; PC 34:1; [M+H]+ ; PC 34:1

23 Name: Agilent Ion Trap XCT ESI; [M H] ; PI 38:4 MW: 885 ID#: 36 DB: Spec. List Comment: PI 38:4; PI(18:0/20:4); Prec: 885.6;

24 Standard phosphatidylethanolamine ESI ( ) PE(17:0/20:4(5Z,8Z,11Z,14Z)) Experimental LMGP _PE_17_20d5d8d11d14_0 ID in LipidBlast First HIT Head to Tail MF=474 RMF=768 LipidBlast PE 37:4; [M-H]-; GPEtn(17:0/ 20:4(5E,8E,1 Name: PE 37:4; [M H] ; GPEtn(17:0/20:4(5E,8E,11E,14E)) equivalent with GPEtn(17:0/20:4(5Z,8Z,11Z,14Z)) MW: 752 ID#: DB: lipidblast neg Comment: Parent= Mz_exact= ; PE 37:4; [M H] ; GPEtn(17:0/20:4(5E,8E,11E,14E)); C42H76NO8P

25 Standard phosphatidylinositol ESI( ) PI(17:0/14:1(9Z)) 100 Experimental LipidBlast sn1 FA sn2 FA [M H] sn2 C6H12O [M H] sn1 C6H12O [M H] sn2 H2O [M H] sn [M H] sn1 H2O [M H] sn LMGP _PI_17_14d9_0017.d, MS Head to Tail MF=344 RMF=524 PI 31:1; [M-H]-; GPIns(14:1(9Z)/ 17:0) ID in LipidBlast First HIT Name: PI 31:1; [M H] ; GPIns(14:1(9Z)/17:0) MW: 793 ID#: DB: lipidblast neg Comment: Parent= Mz_exact= ; PI 31:1; [M H] ; GPIns(14:1(9Z)/17:0); C40H75O13P

26 Standard phosphatidylinositol ESI( ) PI(17:0/20:4(5Z,8Z,11Z,14Z)) Experimental LipidBlast LMGP _PI_17_20d5d8d11d14_ Head to Tail MF=76 RMF=328 ID in LipidBlast First HIT Name: PI 37:4; [M H] ; GPIns(17:0/20:4(5E,8E,11E,14E)) MW: 871 ID#: DB: lipidblast neg Comment: Parent= Mz_exact= ; PI 37:4; [M H] ; GPIns(17:0/20:4(5E,8E,11E,14E)); C46H81O13P sn1 FA sn2 FA [M H] sn2 C6H12O [M H] sn1 C6H12O [M H] sn2 H2O [M H] sn [M H] sn1 H2O [M H] sn1 PI 37:4; [M-H]-; GPIns(17:0/ 20:4(5E,8E,11E

27 Not the END Hands on with course laptops

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