ETISEQ - An algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Wong, Jason W H ^a   Schwahn, Alexander B ^b   Downard, Kevin M ^b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC RANGE; ELUTION PROFILES; INFLUENZA VIRUS; MS/MS ANALYSIS; PEPTIDE FRAGMENTATION; QUANTITATIVE INFORMATION; STANDARD PROTEINS; TRYPTIC DIGESTS;

ALGORITHMS; DATA ACQUISITION; IONS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; VIRUSES;

PEPTIDES;

PEPTIDE DERIVATIVE; PROTEIN DERIVATIVE; TRYPSIN; AVIAN PROTEIN; ION; PEPTIDE FRAGMENT; VIRUS PROTEIN;

ALGORITHM; ARTICLE; AUTOMATION; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; ELUTION; INFLUENZA VIRUS; INFORMATION PROCESSING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEOMICS; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; CHICKEN; INFLUENZA VIRUS A H1N1; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; TANDEM MASS SPECTROMETRY; TIME;

ORTHOMYXOVIRIDAE;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; AVIAN PROTEINS; CHICKENS; INFLUENZA A VIRUS, H1N1 SUBTYPE; IONS; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEOMICS; TANDEM MASS SPECTROMETRY; TIME FACTORS; VIRAL PROTEINS;

EID: 69349092456     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-244     Document Type: Article

References (32)

1. Fenn JB Mann M Meng CK Wong SF Whitehouse CM Electrospray Ionization for Mass-Spectrometry of Large Biomolecules Science 1989, 246(4926):64-71. 10.1126/science.2675315 2675315
2. Aebersold R Mann M Mass spectrometry-based proteomics Nature 2003, 6928:198-207. 10.1038/nature01511 12634793
3. Cravatt BF Simon GM Yates JR The biological impact of mass-spectrometry-based proteomics Nature 2007, 450(7172):991-1000. 10.1038/nature06525 18075578
4. Castro-Perez J Plumb R Granger JH Beattie L Joncour K Wright A Increasing throughput and information content for in vitro drug metabolism experiments using ultra-performance liquid chromatography coupled to a quadrupole time-of-flight mass spectrometer Rapid Commun Mass Spectrom 2005, 19(6):843-848. 10.1002/rcm.1859 15723446
5. Hu QZ Noll RJ Li HY Makarov A Hardman M Cooks RG The Orbitrap: A new mass spectrometer J Mass Spectrom 2005, 40(4):430-443. 10.1002/jms.856 15838939
6. Zubarev RA Kelleher NL McLafferty FW Electron capture dissociation of multiply charged protein cations. A nonergodic process J Am Chem Soc 1998, 120(13):3265-3266. 10.1021/ja973478k
7. Baumgartner C Rejtar T Kullolli M Akella LM Karger BL SeMoP: A new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data J Proteome Res 2008, 7(9):4199-4208. 10.1021/ pr800277y 2556171 18686985
8. Malmström J Lee H Aebersold R Advances in proteomic workflows for systems biology Curr Opin Biotechnol 2007, 18(4):378-384. 10.1016/ j.copbio.2007.07.005 2048812 17698335
9. Wu LF Han DK Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics Expert Rev Proteomics 2006, 3(6):611-619. 10.1586/14789450.3.6.611 17181475
10. Washburn MP Wolters D Yates JR Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat Biotechnol 2001, 19(3):242-247. 10.1038/85686 11231557
11. Gygi SP Rist B Gerber SA Turecek F Gelb MH Aebersold R Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat Biotechnol 1999, 17(10):994-999. 10.1038/13690 10504701
12. Liu HB Sadygov RG Yates JR A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 2004, 76(14):4193-4201. 10.1021/ac0498563 15253663
13. Purvine S Eppel JT Yi EC Goodlett DR Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer Proteomics 2003, 3(6):847-850. 10.1002/pmic.200300362 12833507
14. Venable JD Dong MQ Wohlschlegel J Dillin A Yates JR Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nat Methods 2004, 1(1):39-45. 10.1038/nmeth705 15782151
15. Ramos AA Yang H Rosen LE Yao X Tandem Parallel Fragmentation of Peptides for Mass Spectrometry Anal Chem 2006, 78(18):6391-6397. 10.1021/ ac060672t 16970313
16. Chakraborty AB Berger SJ Gebler JC Use of an integrated MS-multiplexed MS/MS data acquisition strategy for high-coverage peptide mapping studies Rapid Commun Mass Spectrom 2007, 21(5):730-744. 10.1002/rcm.2888 17279597
17. Dongen WDv Wijk JITv Green BN Heerma W Haverkamp J Comparison between collision induced dissociation of electrosprayed protonated peptides in the up-front source region and in a low-energy collision cell Rapid Commun Mass Spectrom 1999, 13(17):1712-1716. 10.1002/ (SICI)1097-0231(19990915)13:17<1712::AID-RCM703>3.0.CO;2-8 10455239
18. McLafferty FW Tandem mass spectrometry Science 1981, 214(4518):280-287. 10.1126/science.7280693 7280693
19. Schlosser A Volkmer-Engert R Volatile polydimethylcyclosiloxanes in the ambient laboratory air identified as source of extreme background signals in nanoelectrospray mass spectrometry J Mass Spectrom 2003, 38(5):523-525. 10.1002/jms.465 12794873
20. Press WH Teukolsky SA Vetterling WT Flannery BP Numerical Recipes: The Art of Scientific Computing Cambridge: Cambridge University Press 3 2007.
21. Eng JK McCormack AL Yates JR An Approach to Correlate Tandem Mass Spectra Data of Peptides with Amino Acid Sequences in a Protein Database J Am Soc Mass Spectrom 1994, 5(11):976. 10.1016/1044-0305(94)80016-2
22. Wong JWH Durante C Cartwright HM Application of fast Fourier transform cross-correlation for the alignment of large chromatographic and spectral datasets Anal Chem 2005, 77(17):5655-5661. 10.1021/ac050619p 16131078
23. Moore DS Basic Practice of Statistics New York: W.H. Freeman and Co 4 2006.
24. NHLBI Proteomics Center at the Institute for Systems Biology http://tools.proteomecenter.org/software.php
25. Mujezinovic N Raidl G Hutchins JRA Peters JM Mechtler K Eisenhaber F Cleaning of raw peptide MS/MS spectra: Improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise Proteomics 2006, 6(19):5117-5131. 10.1002/ pmic.200500928 16955515
26. Kinter M Sherman NE eds Protein Sequencing and Identification Using Tandem Mass Spectrometry New York: Wiley-Interscience 1 2000.
27. Wong JWH Sullivan MJ Cagney G Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments Brief Bioinform 2008, 9(2):156-165. 10.1093/bib/bbm046 17905794
28. Keller A Eng J Zhang N Li XJ Aebersold R A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol Syst Biol 2005, 1. 10.1038/msb4100024 1681455 16729052
29. Tanner S Shu HJ Frank A Wang LC Zandi E Mumby M Pevzner PA Bafna V InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra Anal Chem 2005, 77(14):4626-4639. 10.1021/ac050102d 16013882
30. Craig R Beavis RC TANDEM: Matching proteins with tandem mass spectra Bioinformatics 2004, 20(9):1466-1467. 10.1093/bioinformatics/bth092 14976030
31. Geer LY Markey SP Kowalak JA Wagner L Xu M Maynard DM Yang X Shi W Bryant SH Open mass spectrometry search algorithm J Proteome Res 2004, 3(5):958-964. 10.1021/pr0499491 15473683
32. Elias JE Gygi SP Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Nat Methods 2007, 4(3):207-214. 10.1038/nmeth1019 17327847