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 http://fiehnlab.ucdavis.edu/staff/kind CC-BY License 1
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.
NIST compatible libraries are simply copied as subdirectories under the MSSEARCH directory
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 http://peptide.nist.gov or http://chemdata.nist.gov for more information, software, or MS libraries.
General Library Search view of NIST MS Search GUI
The NIST11 full version has MS/MS tree view
The NIST MS/MS tree view offers the compound view with different ionization voltages
MS/MS search= Precursor filter + similarity filter precursor ion not visible
Similarity match of MS/MS spectrum head to tail view
Head to tail different spectra
Side by side view of MS/MS spectrum
Subtraction view of MS/MS spectrum what are the largest peak differences?
Transfer (right click in NIST MS Search) to MS Interpreter for further inspection
Simple name search not very powerful
Sequential search can find anything
177 spectra with name fragment galactosyl
Powerful sequential search 177 spectra with name fragment galactosyl AND peak at m/z 264 must be between 80% and 100% of base peak
Powerful sequential search: Ten result spectra with modified query
Formula search how many formulae in database?
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 4000 29 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
LipidBlast compound coverage Number positive MS/MS spectra 78314 Number negative MS/MS spectra 134202 Total MS/MS spectra 212516 Total lipid compound number 119200 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 5476 10952 2 0 10952 2 Lysophosphatidylcholines lysopc 80 160 2 0 160 3 Plasmenylphosphatidylcholines plasmenyl PC 222 444 2 0 444 4 Phosphatidylethanolamines PE 5476 16428 3 5476 10952 5 Lysophosphatidylethanolamines lysope 80 240 3 80 160 6 Plasmenylphosphatidylethanolamines plasmenyl PE 222 666 3 222 444 7 Phosphatidylserines PS 5123 15369 3 5123 10246 8 Sphingomyelines SM 168 336 2 0 336 9 Phosphatidic acids PA 5476 16428 3 5476 10952 10 Phosphatidylinositols PI 5476 5476 1 5476 0 11 Phosphatidylglycerols PG 5476 5476 1 5476 0 12 Cardiolipins CL 25426 50852 2 50852 0 13 Ceramide 1 phosphates CerP 168 336 2 168 168 14 Sulfatides ST 168 168 1 168 0 15 Gangliosides [glycan] Cer 880 880 1 880 0 16 Monoacylglycerols MG 74 148 2 0 148 17 Diacylglycerols DG 1764 3528 2 0 3528 18 Triacylglycerols TG 2640 7920 3 0 7920 19 Monogalactosyldiacylglycerols MGDG 5476 21904 4 5476 16428 20 Digalactosyldiacylglycerols DGDG 5476 10952 2 5476 5476 21 Sulfoquinovosyldiacylglycerols SQDG 5476 5476 1 5476 0 22 Diacylated phosphatidylinositol monomannoside Ac2PIM1 144 144 1 144 0 23 Diacylated phosphatidylinositol dimannoside Ac2PIM2 144 144 1 144 0 24 Triacylated phosphatidylinositol dimannoside Ac3PIM2 1728 1728 1 1728 0 25 Tetraacylated phosphatidylinositol dimannoside Ac4PIM2 20736 20736 1 20736 0 26 Diphosphorylated hexaacyl Lipid A LipidA PP 15625 15625 1 15625 0 Total All libraries 119200 212516 50 134202 78314
Example Thermo LTQ; PC 34:1; [M+H]+ ; PC 34:1
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;
Standard phosphatidylethanolamine ESI ( ) PE(17:0/20:4(5Z,8Z,11Z,14Z)) 100 303.233382061271 50 0 196.038106614695 Experimental 466.293757635126 606.219070998728 752.511786311441 466.29354 50 100 269.24790 60 120 180 240 300 360 420 480 540 600 660 720 780 840 LMGP02010003_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#: 108245 DB: lipidblast neg Comment: Parent=752.52306 Mz_exact=752.52306 ; PE 37:4; [M H] ; GPEtn(17:0/20:4(5E,8E,11E,14E)); C42H76NO8P
Standard phosphatidylinositol ESI( ) PI(17:0/14:1(9Z)) 100 Experimental 793.484186423586 269.24827916841 50 152.994186408271 405.239665818928 567.289974906525 0 50 LipidBlast 361.17814 225.18534 999.00 sn1 FA 269.24790 999.00 sn2 FA 361.17814 400.00 [M H] sn2 C6H12O6 405.24070 400.00 [M H] sn1 C6H12O6 523.23097 200.00 [M H] sn2 H2O 541.24153 999.00 [M H] sn2 567.29353 200.00 [M H] sn1 H2O 585.30409 999.00 [M H] sn1 100 225.18534 541.24153 60 120 180 240 300 360 420 480 540 600 660 720 780 840 LMGP06010006_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#: 118720 DB: lipidblast neg Comment: Parent=793.48669 Mz_exact=793.48669 ; PI 31:1; [M H] ; GPIns(14:1(9Z)/17:0); C40H75O13P
Standard phosphatidylinositol ESI( ) PI(17:0/20:4(5Z,8Z,11Z,14Z)) 100 871.531958114408 Experimental 50 303.233059154672 0 152.995721701539 405.241130531344 567.29459414645 980.490276753085 50 100 LipidBlast 269.24790 70 140 210 280 350 420 490 560 630 700 770 840 910 980 LMGP06010004_PI_17_20d5d8d11d14_0 405.24077 585.30416 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#: 119197 DB: lipidblast neg Comment: Parent=871.53368 Mz_exact=871.53368 ; PI 37:4; [M H] ; GPIns(17:0/20:4(5E,8E,11E,14E)); C46H81O13P 269.24790 999.00 sn1 FA 303.23226 999.00 sn2 FA 405.24077 400.00 [M H] sn2 C6H12O6 439.22513 400.00 [M H] sn1 C6H12O6 567.29360 200.00 [M H] sn2 H2O 585.30416 999.00 [M H] sn2 601.27796 200.00 [M H] sn1 H2O 619.28852 999.00 [M H] sn1 PI 37:4; [M-H]-; GPIns(17:0/ 20:4(5E,8E,11E
Not the END Hands on with course laptops