Optimization of the use of consensus methods for the detection and putative identification of peptides via mass-spectrometry using protein standard mixtures

Journal of Proteomics and Bioinformatics

Volumn 2, Issue 6, 2009, Pages 262-273

  Sultana, Tamanna ^a   Jordan, Rick ^a   Lyons Weiler, James ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics; Comparative evaluation; Consensus methods; Consensus set; Mass spectrometry; Peptide identification; Proteomics

Indexed keywords

EID: 75649142942     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000085     Document Type: Article

References (21)

1. Alves G, Wu WW, Wang G, Shen RF, Yu YK (2008) Enhancing peptide identification confidence by combining search methods. J Proteome Research 7: 3102-3113.
2. Balgley BM, Laudeman T, Yang L, Song T, Lee CS (2007) Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy. Mol Cell Proteomics 6: 1599-1608.
3. Boutilier K, Ross M, Podtelejnikov AV, Orsi C, Taylor R, (2005) Comparison of different search engines using validated MS/MS test datasets. Anal Chim Acta 534: 11-20.
4. Chamrad DC, Körting G, Stühler K, Meyer HE, Klose J, (2004) Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 4: 619-628.
5. Craig R and Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20: 1466-1467.
6. Eng JK, McCormack AL, Yates JR III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989.
7. Jiang X, Jiang X, Han G, Ye M, Zou H (2007) Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. BMC Bioinformatics 8: 323-334.
8. Johnson RS, Davis MT, Tayler JA, Patterson SD (2005) Informatics for protein identification by mass spectrometry. Methods 35: 223-236.
9. Kapp EA, Schutz F, Connolly LM, Chakel JA, Meza JE, (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity of analysis. Proteomics 5: 3475-3490.
10. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392.
11. Lyons-Weiler J (2005) Standards of excellence and open questions in cancer biomarker research: an informatics perspective. Cancer Informatics 1: 1-7.
12. MacCoss MJ, Wu CC, Yates JR III (2002) Probabilitybased validation of protein identifications using a modified SEQUEST algorithm. Anal Chem 74: 5593-5599.
13. Moore RE, Young MK, Lee TD (2003) Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom 12: 378-386.
14. Nesvizhskii AI, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75: 4646-4658.
15. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
16. Resing K, Meyer-Arendt K, Mendoza AM, Aveline-wolf LD, Jonscher KR, (2004) Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem 76: 3556-3568.
17. Rohrbough J, Breci L, Merchant N, Miller S, Haynes PA (2006) Verification of single-peptide protein identification by the application of complementary search algorithms. J. Biomolecular Techniques 17: 327-332.
18. Rudnick PA, Wang Y, Evans EL, Lee CS, Balgley BM (2005) Large scale analysis of MASCOT results using a mass accuracy-based threshold (MATH) effectively improves data interpretation. J Proteome Res 4: 1353-1360.
19. Sadygov RG, Cociorva D, Yates JR III (2004) Largescale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods 1: 195-202.
20. Searle BC, Turner M, Nesvizhskii AI (2008) Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Research 7: 245-253.
21. Searle BC, Dasari S, Turner M, Reddy AP, Choi D, (2004) High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. Anal Chem 76: 2220-2230.