YADA: A tool for taking the most out of high-resolution spectra

Bioinformatics

Volumn 25, Issue 20, 2009, Pages 2734-2736

  Carvalho, Paulo C ^a,b   Xu, Tao ^b   Han, Xuemei ^b   Cociorva, Daniel ^b   Barbosa, Valmir C ^a   Yates III, John R ^b  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; HIGH THROUGHPUT SCREENING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MASS SPECTROMETRY; PEPTIDES; PROTEOMICS; SOFTWARE;

EID: 70350018231     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp489     Document Type: Article

References (14)

1. Boyne,M.T. et al. (2009) Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval. J. Proteome Res., 8, 374-379.
2. Carvalho,P.C. et al. (2009) Charge prediction machine: Tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal. Chem., 81, 1996-2003.
3. Carvalho,P.C. et al. (2008) PatternLab for proteomics: A tool for differential shotgun proteomics. BMC Bioinformatics, 9, 316.
4. Chen,L. and Yap,Y.L. (2008) Automated charge state determination of complex isotope-resolved mass spectra by peak-target Fourier transform. J. Am. Soc. Mass Spectrom., 19, 46-54.
5. Chi,A. et al. (2007) Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl Acad. Sci. USA, 104, 2193-2198.
6. Cociorva,D. et al. (2007) Validation of tandem mass spectrometry database search results using DTASelect. Curr. Protoc. Bioinformatics Chapter 13, Unit 13.4.
7. Eng,J.K. et al. (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.
8. Forbes,A.J. et al. (2001) Toward efficient analysis of>70 kDa proteins with 100% sequence coverage. Proteomics, 1, 927-933.
9. Horn,D.M. et al. (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom., 11, 320-332.
10. Makarov,A. (2000) Electrostatic axially harmonic orbital trapping: A high-performance technique of mass analysis. Anal. Chem., 72 1156-1162.
11. Mayampurath,A.M. et al. (2008) DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics, 24, 1021-1023.
12. McDonald,W.H. et al. (2004) MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18, 2162-2168.
13. Perkins,D.N. et al. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3567.
14. Xu,T. et al. (2006) ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program. Mol. Cell. Proteomics 5, S174.