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Volumn 10, Issue 7, 2011, Pages 2930-2936

PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; MASS SPECTROMETRY; PEAKSPTM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN MODIFICATION;

EID: 79960010160     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200153k     Document Type: Article
Times cited : (143)

References (29)
  • 1
    • 77954513767 scopus 로고    scopus 로고
    • The pros and cons of peptide-centric proteomics
    • Duncan, M.; Aebersold, R.; Caprioli, R. The pros and cons of peptide-centric proteomics Nat. Biotechnol. 2010, 28 (7) 659-664
    • (2010) Nat. Biotechnol. , vol.28 , Issue.7 , pp. 659-664
    • Duncan, M.1    Aebersold, R.2    Caprioli, R.3
  • 2
    • 0019376492 scopus 로고
    • In vivo chemical modification of proteins
    • Wold, F. In vivo chemical modification of proteins Annu. Rev. Biochem. 1981, 50, 783-814
    • (1981) Annu. Rev. Biochem. , vol.50 , pp. 783-814
    • Wold, F.1
  • 3
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • DOI 10.1002/pmic.200300744
    • Creasy, D. M.; Cottrell, J. S. Unimod: Protein modifications for mass spectrometry Proteomics 2004, 4 (6) 1534-1536 (Pubitemid 38738312)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 4
    • 79959925193 scopus 로고    scopus 로고
    • ABRF Delta Mass database;; Last accessed Nov
    • ABRF Delta Mass database; http://www.abrf.org/index.cfm/dm.home; Last accessed Nov. 2010.
    • (2010)
  • 5
    • 0037726623 scopus 로고    scopus 로고
    • A major step on the road to understanding a unique posttranslational modification and its role in a genetic disease
    • DOI 10.1016/S0092-8674(03)00354-4
    • Baenziger, J. U. A major step on the road to understanding a unique posttranslational modification and its role in a genetic disease Cell 2003, 113, 421-422 (Pubitemid 36588743)
    • (2003) Cell , vol.113 , Issue.4 , pp. 421-422
    • Baenziger, J.U.1
  • 6
    • 0037338365 scopus 로고    scopus 로고
    • Proteomic analysis of post-translational modifications
    • DOI 10.1038/nbt0303-255
    • Mann, M.; Jensen, O. Proteomic analysis of post-translational modifications Nat. Biotechnol. 2003, 21 (3) 255-261 (Pubitemid 36314808)
    • (2003) Nature Biotechnology , vol.21 , Issue.3 , pp. 255-261
    • Mann, M.1    Jensen, O.N.2
  • 7
    • 35848970747 scopus 로고    scopus 로고
    • Mapping protein post-translational modifications with mass spectrometry
    • DOI 10.1038/nmeth1100, PII NMETH1100
    • Witze, E. S.; Old, W. M.; Resing, K. A.; Ahn, N. G. Mapping protein post-translational modifications with mass spectrometry Nat. Methods 2007, 4 (10) 798-806 (Pubitemid 350055576)
    • (2007) Nature Methods , vol.4 , Issue.10 , pp. 798-806
    • Witze, E.S.1    Old, W.M.2    Resing, K.A.3    Ahn, N.G.4
  • 8
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence database using mass spectrometry data Electrophoresis 1999, 20, 3551-3567 (Pubitemid 30007252)
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 9
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Enga, J. K.; McCormacka, A. L.; Yates, J. R., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5 (11) 976-989
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , Issue.11 , pp. 976-989
    • Enga, J.K.1    McCormacka, A.L.2    Yates III, J.R.3
  • 10
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • DOI 10.1093/bioinformatics/bth092
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-1467 (Pubitemid 38931421)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 13
    • 0029644596 scopus 로고
    • Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
    • Yates, J. R., III.; Eng, J. K.; McCormack, A. L.; Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database Anal. Chem. 1995, 67 (8) 1426-1436
    • (1995) Anal. Chem. , vol.67 , Issue.8 , pp. 1426-1436
    • Yates III, J.R.1    Eng, J.K.2    McCormack, A.L.3    Schieltz, D.4
  • 14
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • DOI 10.1021/ac050102d
    • Tanner, S.; Shu, H; Frank, A.; Wang, L. -C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra Anal. Chem. 2005, 77, 4626-4639 (Pubitemid 41542287)
    • (2005) Analytical Chemistry , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 15
    • 0028575316 scopus 로고
    • Error-tolerant identification of peptides in sequence databases by peptide sequence tags
    • Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags Anal. Chem. 1994, 66 (24) 4390-4399 (Pubitemid 124006101)
    • (1994) Analytical Chemistry , vol.66 , Issue.24 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 16
    • 0345600791 scopus 로고    scopus 로고
    • GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model
    • DOI 10.1021/ac0347462
    • Tabb, D. L.; Saraf, A.; Yates, J. R., III. GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model Anal. Chem. 2003, 75, 6415-6421 (Pubitemid 37493895)
    • (2003) Analytical Chemistry , vol.75 , Issue.23 , pp. 6415-6421
    • Tabb, D.L.1    Saraf, A.2    Yates III, J.R.3
  • 17
    • 1942423061 scopus 로고    scopus 로고
    • High-Throughput Identification of Proteins and Unanticipated Sequence Modifications Using a Mass-Based Alignment Algorithm for MS/MS de Novo Sequencing Results
    • DOI 10.1021/ac035258x
    • Searle, B. C.; Dasari, S.; Turner, M.; Reddy, A. P.; Choi, D.; Wilmarth, P. A.; McCormack, A. L.; David, L. L.; Nagalla, S. R. High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results Anal. Chem. 2004, 76, 2220-2230 (Pubitemid 38496062)
    • (2004) Analytical Chemistry , vol.76 , Issue.8 , pp. 2220-2230
    • Searle, B.O.1    Dasari, S.2    Turner, M.3    Reddy, A.P.4    Choi, D.5    Wilmarth, P.A.6    McCormack, A.L.7    David, L.L.8    Nagalla, S.B.9
  • 18
    • 22544465253 scopus 로고    scopus 로고
    • Spider: Software for protein identification from sequence tags with de novo sequencing error
    • DOI 10.1142/S0219720005001247, PII S0219720005001247
    • Han, Y.; Ma, B.; Zhang, K. SPIDER: software for protein identification from sequence tags containing de novo sequencing error J. Bioinform. Comput. Biol. 2005, 3 (3) 697-716 (Pubitemid 41015284)
    • (2005) Journal of Bioinformatics and Computational Biology , vol.3 , Issue.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 20
    • 33847234661 scopus 로고    scopus 로고
    • Lookup Peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry
    • Bern, M.; Cai, Y.; Goldberg, D. Lookup Peaks: A hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry Anal. Chem. 2007, 79, 1393-1400
    • (2007) Anal. Chem. , vol.79 , pp. 1393-1400
    • Bern, M.1    Cai, Y.2    Goldberg, D.3
  • 21
    • 34848889259 scopus 로고    scopus 로고
    • The paragon algorithm, a next generation search engine that uses sequence temperature values sequence temperature values and feature probabilities to identify peptides from tandem mass spectra
    • DOI 10.1074/mcp.T600050-MCP200
    • Shilov, I. V.; Seymour, S. L.; Patel, A. A.; Loboda, A.; Tang, W. H.; Keating, S. P.; Hunter, C. L.; Nuwaysir, L. M.; Schaeffer, D. A. The Paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra Mol. Cell. Proteomics 2007, 6, 1638-1655 (Pubitemid 47506173)
    • (2007) Molecular and Cellular Proteomics , vol.6 , Issue.9 , pp. 1638-1655
    • Shilov, I.V.1    Seymourt, S.L.2    Patel, A.A.3    Loboda, A.4    Tang, W.H.5    Keating, S.P.6    Hunter, C.L.7    Nuwaysir, L.M.8    Schaeffer, D.A.9
  • 22
    • 0036807449 scopus 로고    scopus 로고
    • Error tolerant searching of uninterpreted tandem mass spectrometry data
    • DOI 10.1002/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO;2-5
    • Creasy, D. M; Cottrell, J. S. Error tolerant searching of uninterpreted tandem mass spectrometry data Proteomics 2002, 2, 1426-1434 (Pubitemid 35340023)
    • (2002) Proteomics , vol.2 , Issue.10 , pp. 1426-1434
    • Creasy, D.M.1    Cottrell, J.S.2
  • 23
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications by blind search of mass spectra
    • DOI 10.1038/nbt1168
    • Tsur, D.; Tanner, S.; Zandi, E.; Bafna, V.; Pevzner, P. A. Identification of post-translational modifications by blind search of mass spectra Nat. Biotechnol. 2005, 23, 1562-1567 (Pubitemid 41752935)
    • (2005) Nature Biotechnology , vol.23 , Issue.12 , pp. 1562-1567
    • Tsur, D.1    Tanner, S.2    Zandi, E.3    Bafna, V.4    Pevzner, P.A.5
  • 24
    • 33646903914 scopus 로고    scopus 로고
    • ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
    • Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures Mol. Cell. Proteomics 2006, 5, 935-947
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 935-947
    • Savitski, M.M.1    Nielsen, M.L.2    Zubarev, R.A.3
  • 26
    • 70349925705 scopus 로고    scopus 로고
    • Reanalysis of tyrannosaurus rex mass spectra
    • Bern, M.; Phinney, B. S.; Goldberg, D. Reanalysis of tyrannosaurus rex mass spectra J. Proteome Res. 2009, 8, 4328-4332
    • (2009) J. Proteome Res. , vol.8 , pp. 4328-4332
    • Bern, M.1    Phinney, B.S.2    Goldberg, D.3
  • 28
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • DOI 10.1021/ac025747h
    • Keller, A.; Nesvizhskii, A.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392 (Pubitemid 35215372)
    • (2002) Analytical Chemistry , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 29
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • DOI 10.1021/pr700600n
    • Käll, L.; Storey, J. D.; MacCoss, M. J.; Noble, W. S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases J. Proteome Res. 2008, 7 (01) 29-34 (Pubitemid 351171110)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 29-34
    • Kall, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4


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