Optimization-based peptide mass fingerprinting for protein mixture identification

Journal of Computational Biology

Volumn 17, Issue 3, 2010, Pages 221-235

  He, Zengyou ^a   Yang, Chao ^a   Yang, Can ^a   Qi, Robert Z ^a   Tam, Jason Po Ming ^a   Yu, Weichuan ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Mass spectrometry; Peptide mass fingerprinting; Protein identification; Proteomics

Indexed keywords

PEPTIDE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; COMPUTER SIMULATION; CONFERENCE PAPER; METHODOLOGY; MOLECULAR WEIGHT; PEPTIDE MAPPING; TANDEM MASS SPECTROMETRY; TIME;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; MOLECULAR WEIGHT; PEPTIDE MAPPING; PEPTIDES; PROTEINS; TANDEM MASS SPECTROMETRY; TIME FACTORS;

EID: 77950829370     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0160     Document Type: Conference Paper

References (18)

1. Aebersold, R., and Mann, M. 2003. Mass spectrometry-based proteomics. Nature 422, 198-207. (Pubitemid 36362757)
2. Berndt, P., Hobohm, U., and Langen, H. 1999. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20, 3521-3526. (Pubitemid 30007249)
3. Clauser, K.R., Baker, P., and Burlingame, A.L. (1999). Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882. (Pubitemid 29340480)
4. Eriksson, J., and Fenyö, D. 2004. Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results. J. Proteome Res. 3, 32-36. (Pubitemid 38233447)
5. Eriksson, J., and Fenyö , D. 2005. Protein identification in complex mixtures. J. Proteome Res. 4, 387-393. (Pubitemid 40548143)
6. Henzel, W.J., Billeci, T.M., Stults, J.T., et al. 1993. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Nat. Acad. Sci. USA 90, 5011-5015.
7. Jaitly, N., Mayampurath, A., Littlefield, K., et al. 2009. Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinform. 10, 87.
8. James, P., Quadroni, M., Carafoli, E., et al. 1993. Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 195, 58-64.
9. Jensen, O.N., Podtelejnikov, A.V., and Mann, M. 1997. Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal. Chem. 69, 4741-4750. (Pubitemid 127485122)
10. Mann, M., Hojrup, P., and Roepstorff, P. 1993. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 22, 338-345. (Pubitemid 23165446)
11. Monroe, M.E., Tolic, N., Jaitly, N., et al. 2007. VIPER: an advanced software package to support high-throughput LCMS peptide identification. Bioinformatics 23, 2021-2023. (Pubitemid 47299846)
12. Pappin, D.J., Hojrup, P., and Bleasby, A.J. 1993. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, 327-332.
13. Park, Z.Y., and Russell, D.H. 2001. Identification of individual proteins in complex protein mixtures by highresolution, high-mass-accuracy MALDI TOF-mass spectrometry analysis of in-solution thermal denaturation/enzymatic digestion. Anal. Chem. 73, 2558-2564.
14. Perkins, D.N., Pappin, D.J.C., Creasy, D.M., et al. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567.
15. Samuelsson, J., Dalevi, D., Levander, F., et al. 2004. Modular, scriptable and automated analysis tools for highthroughput peptide mass fingerprinting. Bioinformatics 20, 3628-3635. (Pubitemid 40136799)
16. Wool, A., and Smilansky, Z. 2002. Precalibration of matrix-assisted laser desorption/ionization-time of flight spectra for peptide mass fingerprinting. Proteomics 2, 1365-1373. (Pubitemid 35340018)
17. Yates, J.R., Speicher, S., Griffin, P.R., et al. 1993. Peptide mass maps: a highly informative approach to protein identification. Anal. Biochem. 214, 297-408. (Pubitemid 23336396)
18. Zhang, W., and Chait, B.T. 2000. Profound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72, 2482-2489. (Pubitemid 30395651)