Modeling and characterization of multi-charge mass spectra for peptide sequencing

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 6, 2006, Pages 1329-1352

  Chong, Ket Fah ^a   Ning, Kang ^a   Leong, Hon Wai ^a   Pevzner, Pavel ^b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Analysis and characterization; Multi charge spectra; Peptide sequencing

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; PREDICTION; PROTEIN ANALYSIS; PROTEOMICS; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; MASS SPECTROMETRY; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PEPTIDES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 33846550808     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S021972000600248X     Document Type: Article

References (12)

1. Craig R, Cortens JP, Beavis RC, Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3:1234-1242, 2004.
2. Dancik V, Addona T, Clauser K, Vath J, Pevzner P, De novo protein sequencing via tandem mass-spectrometry, J Comp Biol 6:327-341, 1999.
3. Eng JK, McCormack AL, Yates JR, An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, JASMS 5:976-989, 1994.
4. Frank A, Pevzner P, Pepnovo: De novo peptide sequencing via probabilistic network modeling, Anal Chem 77:964-973, 2005.
5. Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E, Experimental protein mixture for validating tandem mass spectral analysis, OMICS 6:207-212, 2002.
6. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G, Peaks: Powerful software for peptide de novo sequencing by ms/ms, Rapid Communications in Mass Spectrometry 17:2337-2342, 2003.
7. Mann M, Wilm M, Error-tolerant identification of peptides in sequence databases by peptide sequence tags, Anal Chem 66:4390-4399, 1994.
8. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis 20:3551-3567, 1999.
9. Tang H, Private communications, 2006.
10. Taylor JA, Johnson RS, Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry, Anal Chem, 73:2594-2604, 2001.
11. The GPM Web-site. ftp://ftp.thegpm.org/quartz
12. The ISB Web-site. http://www.systemsbiology.org/extra/ protein-mixture.html.