Informatics of protein and posttranslational modification detection via shotgun proteomics

Methods in Molecular Biology

Volumn 1002, Issue , 2013, Pages 167-179

  Holman, Jerry D ^a   Dasari, Surendra ^a   Tabb, David L ^a  

^a VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Database search; Posttranslational modi fi cation; Protein identi fi cation; Proteome informatics; Sequence tagging; Shotgun proteomics; Software

Indexed keywords

COMPUTER PROGRAM; INFORMATION SCIENCE; LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN DATABASE; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY;

ALGORITHMS; AMINO ACID SEQUENCE; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; HUMANS; MASS SPECTROMETRY; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 84892759537     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-360-2_14     Document Type: Review

References (15)

1. Eng JK, McCormack AL, Yates JR (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
2. Yates JR, Eng JK, McCormack AL, Schieltz D (1995) Method to correlate tandem mass spectra of modi fi ed peptides to amino acid sequences in the protein database. Anal Chem 67:1426-1436
3. Craig R, Beavis RC (2003) A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 17:2310-2316
4. Mann M, Wilm M (1994) Error-tolerant identi fi cation of peptides in sequence databases by peptide sequence tags. Anal Chem 66:4390-4399
5. Tabb DL, Saraf A, Yates JR (2003) GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem 75:6415-6421
6. Tanner S, Shu H, Frank A et al (2005) InsPecT: identi fi cation of posttranslationally modi fi ed peptides from tandem mass spectra. Anal Chem 77:4626-4639
7. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA (2005) Identi fi cation of post-translational modi fi cations by blind search of mass spectra. Nat Biotechnol 23:1562-1567
8. Dasari S, Chambers MC, Codreanu SG et al (2011) Sequence tagging reveals unexpected modi fi cations in toxicoproteomics. Chem Res Toxicol 24:204-216
9. Tabb DL, Fernando CG, Chambers MC (2007) MyriMatch: highly accurate tandem mass spectral peptide identi fi cation by multivariate hypergeometric analysis. J Proteome Res 6:654-661
10. Tabb DL, Ma Z-Q, Martin DB, Ham A-JL, Chambers MC (2008) DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 7:3838-3846
11. Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham A-JL, Tabb DL (2010) TagRecon: high-throughput mutation identi fi cation through sequence tagging. J Proteome Res 9:1716-1726
12. Zhang B, Chambers MC, Tabb DL (2007) Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 6:3549-3557
13. Ma Z-Q, Dasari S, Chambers MC et al (2009) IDPicker 2.0: improved protein assembly with high discrimination peptide identi fi cation fi ltering. J Proteome Res 8:3872-3881
14. Holman JD, Ma Z-Q, Tabb DL (2012) Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker, Current protocols in bioinformatics/ editorial board, Andreas D. Baxevanis. Chapter 13, Unit 13.17
15. Sprung RW Jr, Brock JWC, Tanksley JP et al (2009) Equivalence of protein inventories obtained from formalin- fi xed paraf fi nembedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics 8:1988-1998