High-accuracy peptide mass fingerprinting using peak intensity data with machine learning

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 62-69

  Yang, Dongmei ^a   Ramkissoon, Kevin ^a   Hamlett, Eric ^a   Giddings, Morgan C ^a,b,c,d  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b USA and North Carolina State University   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

^d NONE   (United States)

Author keywords

Ion suppression; Mass spectrometry; Peak intensity; Peptide mass fingerprinting; Protein identification

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; MACHINE LEARNING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DETERMINATION; VALIDATION STUDY;

ARTIFICIAL INTELLIGENCE; DATA INTERPRETATION, STATISTICAL; PEPTIDE MAPPING; PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 38649136585     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070088g     Document Type: Article

References (20)

1. Giddings, M. C.; Shah, A. A.; Gesteland, R.; Moore, B. Genome-based peptide fingerprint scanning. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (1), 20-25.
2. Mann, M.; Hojrup, P.; Roepstorff, P. Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 1993, 22 (6), 338-345.
3. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
4. Wilkins, M. R.; Gasteiger, E.; Wheeler, C. H.; Lindskog, I.; Sanchez, J. C.; Bairoch, A.; Appel, R. D.; Dunn, M. J.; Hochstrasser, D. F. Multiple parameter cross-species protein identification using MultiIdent - a world-wide web accessible tool. Electrophoresis 1998, 19 (18), 3199-3206.
5. Annesley, T. M. Ion suppression in mass spectrometry. Clin. Chem. 2003, 49 (7), 1041-1044.
6. King, R.; Bonfiglio, R.; Fernandez-Metzler, C.; Miller-Stein, C.; Olah, T. Mechanistic investigation of ionization suppression in electrospray ionization. J. Am. Soc. Mass Spectrom. 2000, 11 (11), 942-950.
7. Gay, S.; Binz, P. A.; Hochstrasser, D. F.; Appel, R. D. Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2002, 2 (10), 1374-1391.
8. Rabiner, L. R. A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition. Proc. IEEE 1989, 77 (2), 257-286.
9. Wisz, M. S.; Suarez, M. K.; Holmes, M. R.; Giddings, M. C. GFSWeb: a web tool for genome-based identification of proteins from mass spectrometric samples. J. Proteome Res. 2004, 3 (6), 1292-1295.
10. Blattner, F. R.; Plunkett, G., III; Bloch, C. A.; Perna, N. T.; Burland, V.; Riley, M.; Collado-Vides, J.; Glasner, J. D.; Rode, C. K.; Mayhew, G. F.; Gregor, J.; Davis, N. W.; Kirkpatrick, H. A.; Goeden, M. A.; Rose, D. J.; Mau, B.; Shao, Y. The complete genome sequence of Escherichia coli K-12. Science 1997, 277 (5331), 1453-1474.
11. MSDB: Mass Spectrometry protein sequence DataBase. http://csc-fserve.hh. med.ic.ac.uk/msdb.html(2/15/07),
12. Eriksson, J.; Chait, B. T.; Fenyo, D. A statistical basis for testing the significance of mass spectrometric protein identification results. Anal. Chem. 2000, 72 (5), 999-1005.
13. Fenyo, D.; Beavis, R. C. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75 (4), 768-774.
14. Karp, P. D.; Riley, M.; Saier, M.; Paulsen, I. T.; Collado-Vides, J.; Paley, S. M.; Pellegrini-Toole, A.; Bonavides, C.; Gama-Castro, S. The EcoCyc Database. Nucleic Acids Res. 2002, 30 (1), 56-58.
15. Agresti, A.C. B. Approximate is better than "Exact"for interval estimation of biomial proportions. The American Statistician 1998, 52, 119-126.
16. Olsen, J. V.; Ong, S. E.; Mann, M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3 (6), 608-614.
17. Hanley, J. A.; McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982, 143 (1), 29-36.
18. Sechi, S.; Chait, B. T. Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification. Anal. Chem. 1998, 70 (24), 5150-5158.
19. Krause, E.; Wenschuh, H.; Jungblut, P. R. The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. Anal. Chem. 1999, 71 (19), 4160-4165.
20. Hosmer D. W.; Lemeshow, S. Applied Logistic Regression; John Wiley & Sons: New York, 1989.