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Volumn 29, Issue 24, 2013, Pages 3199-3203

MS2PIP: A tool for MS/MS peak intensity prediction

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN;

EID: 84893048557     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt544     Document Type: Article
Times cited : (107)

References (20)
  • 1
    • 36348959863 scopus 로고    scopus 로고
    • A machine learning approach to predicting peptide fragmentation spectra
    • Arnold, R.J. et al. (2006) A machine learning approach to predicting peptide fragmentation spectra. In: Pacific Symposium on Biocomputing. pp. 219-230.
    • (2006) Pacific Symposium on Biocomputing , pp. 219-230
    • Arnold, R.J.1
  • 2
    • 59149100438 scopus 로고    scopus 로고
    • Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors
    • Barton, S.J. and Whittaker, J.C. (2009) Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors. Mass Spectrom. Rev., 28, 177-187.
    • (2009) Mass Spectrom. Rev. , vol.28 , pp. 177-187
    • Barton, S.J.1    Whittaker, J.C.2
  • 3
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. (2001) Random Forests. Machine Learning, 45, 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 4
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R. and Beavis, R.C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 5
    • 79952308634 scopus 로고    scopus 로고
    • A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods
    • Degroeve, S. et al. (2011) A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods. Proteomics, 11, 1172-1180.
    • (2011) Proteomics , vol.11 , pp. 1172-1180
    • Degroeve, S.1
  • 6
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • Elias, J.E. et al. (2004) Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol., 22, 214-219.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 214-219
    • Elias, J.E.1
  • 7
    • 7044246160 scopus 로고    scopus 로고
    • Open mass spectrometry search algorithm
    • Geer, L.Y. et al. (2004) Open mass spectrometry search algorithm. J. Proteome Res., 3, 958-964.
    • (2004) J. Proteome Res. , vol.3 , pp. 958-964
    • Geer, L.Y.1
  • 8
    • 77949750038 scopus 로고    scopus 로고
    • Ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
    • Helsens, K. et al. (2010) ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics, 10, 1261-1264.
    • (2010) Proteomics , vol.10 , pp. 1261-1264
    • Helsens, K.1
  • 9
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam, H. et al. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics, 7, 655-667.
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1
  • 10
    • 79952152636 scopus 로고    scopus 로고
    • On the accuracy and limits of peptide fragmentation spectrum prediction
    • Li, S. et al. (2011) On the accuracy and limits of peptide fragmentation spectrum prediction. Anal. Chem., 83, 790-796.
    • (2011) Anal. Chem. , vol.83 , pp. 790-796
    • Li, S.1
  • 11
    • 28544433960 scopus 로고    scopus 로고
    • MASPIC: Intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence
    • Narasimhan, C. et al. (2005) MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Anal. Chem., 77, 7581-7593.
    • (2005) Anal. Chem. , vol.77 , pp. 7581-7593
    • Narasimhan, C.1
  • 12
    • 76649122499 scopus 로고    scopus 로고
    • Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance
    • Paulovich, A.G. et al. (2010) Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol. Cell. Proteomics, 9, 242-254.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 242-254
    • Paulovich, A.G.1
  • 13
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D.N. et al. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1
  • 14
    • 30044442277 scopus 로고    scopus 로고
    • Central limit theorem as an approximation for intensity based scoring function
    • Sadygov, R. et al. (2006) Central limit theorem as an approximation for intensity based scoring function. Anal. Chem., 78, 89-95.
    • (2006) Anal. Chem. , vol.78 , pp. 89-95
    • Sadygov, R.1
  • 15
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • Tabb, D.L. et al. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res., 6, 654-661.
    • (2007) J. Proteome Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1
  • 16
    • 84885651630 scopus 로고    scopus 로고
    • Getting intimate with trypsin, the leading protease in proteomics
    • Epub ahead of print June 15, 2013
    • Vandermarliere, E. et al. (2013) Getting intimate with trypsin, the leading protease in proteomics. Mass Spectrom. Rev., [Epub ahead of print, doi:10.1002/mas.21376, June 15, 2013].
    • (2013) Mass Spectrom. Rev.
    • Vandermarliere, E.1
  • 17
    • 79955761196 scopus 로고    scopus 로고
    • Peptide identification quality control
    • Vaudel, M. et al. (2011) Peptide identification quality control. Proteomics, 11, 2105-2114.
    • (2011) Proteomics , vol.11 , pp. 2105-2114
    • Vaudel, M.1
  • 18
    • 3242660851 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides
    • Zhang, Z. (2004) Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem., 76, 3908-3922.
    • (2004) Anal. Chem. , vol.76 , pp. 3908-3922
    • Zhang, Z.1
  • 19
    • 26444607864 scopus 로고    scopus 로고
    • Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges
    • Zhang, Z. (2005) Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem., 77, 6364-6373.
    • (2005) Anal. Chem. , vol.77 , pp. 6364-6373
    • Zhang, Z.1
  • 20
    • 51249111303 scopus 로고    scopus 로고
    • A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
    • Zhou, C. et al. (2008) A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data. BMC Bioinformatics, 9, 325.
    • (2008) BMC Bioinformatics , vol.9 , pp. 325
    • Zhou, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.