메뉴 건너뛰기




Volumn 5, Issue 12, 2012, Pages 285-291

Modls: Post-translational modification localization scoring with automatic specificity expansion

Author keywords

Algorithm; Localization; Open source; Phosphorylation; Pipeline; PTM

Indexed keywords

ALGORITHM; ARTICLE; AUTOMATIC SPECIFICITY EXPANSION; COMPUTER PROGRAM; HYDROXYLATION; INFORMATION PROCESSING; MASS SPECTROMETRY; POSTTRANSLATIONAL MODIFICATION LOCALIZATION SCORING; PROTEIN DATABASE; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; SEARCH ENGINE;

EID: 84872332086     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000251     Document Type: Article
Times cited : (6)

References (25)
  • 1
    • 33749853607 scopus 로고    scopus 로고
    • A probabilitybased approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (2006) A probabilitybased approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24: 1285-1292.
    • (2006) Nat Biotechnol , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villén, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 2
    • 4544370533 scopus 로고    scopus 로고
    • Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation
    • U S A
    • Olsen JV, Mann M (2004) Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A 101: 13417-134122.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 13417-134122
    • Olsen, J.V.1    Mann, M.2
  • 3
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, et al. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5
  • 4
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat Biotechnology 26: 1367-1372.
    • (2008) Nat Biotechnology , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 5
    • 65249185673 scopus 로고    scopus 로고
    • SLoMo: Automated site localization of modifications from ETD/ECD mass spectra
    • Bailey CM, Sweet SM, Cunningham DL, Zeller M, Heath JK, et al. (2009) SLoMo: automated site localization of modifications from ETD/ECD mass spectra. J Proteome Res 8: 1965-1971.
    • (2009) J Proteome Res , vol.8 , pp. 1965-1971
    • Bailey, C.M.1    Sweet, S.M.2    Cunningham, D.L.3    Zeller, M.4    Heath, J.K.5
  • 6
    • 82755182013 scopus 로고    scopus 로고
    • Universal and confident phosphorylation site localization using phosphoRS
    • Taus T, Köcher T, Pichler P, Paschke C, Schmidt A, et al. (2011) Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 10: 5354-5362.
    • (2011) J Proteome Res , vol.10 , pp. 5354-5362
    • Taus, T.1    Köcher, T.2    Pichler, P.3    Paschke, C.4    Schmidt, A.5
  • 8
    • 84860879590 scopus 로고    scopus 로고
    • Modification site localization scoring: Strategies and performance
    • Chalkley RJ, Clauser KR (2012) Modification site localization scoring: strategies and performance. Mol Cell Proteomics 11: 3-14.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 3-14
    • Chalkley, R.J.1    Clauser, K.R.2
  • 10
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • Creasy DM, Cottrell JS (2004) Unimod: Protein modifications for mass spectrometry. Proteomics 4: 1534-1536.
    • (2004) Proteomics , vol.4 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 11
    • 43649093915 scopus 로고    scopus 로고
    • Oxygen sensing by metazoans: The central role of the HIF hydroxylase pathway
    • Kaelin WG Jr, Ratcliffe PJ (2008) Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell 30: 393-402.
    • (2008) Mol Cell , vol.30 , pp. 393-402
    • Kaelin Jr., W.G.1    Ratcliffe, P.J.2
  • 12
    • 77953911347 scopus 로고    scopus 로고
    • Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: Chemical artifact or post-translational modification?
    • Perdivara I, Deterding LJ, Przybylski M, Tomer KB (2010) Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: chemical artifact or post-translational modification? J Am Soc Mass Spectrom 21: 1114-1117.
    • (2010) J Am Soc Mass Spectrom , vol.21 , pp. 1114-1117
    • Perdivara, I.1    Deterding, L.J.2    Przybylski, M.3    Tomer, K.B.4
  • 14
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/ MS analysis platform utilizing open XML file formats
    • Keller A, Eng J, Zhang N, Li XJ, Aebersold R (2005) A uniform proteomics MS/ MS analysis platform utilizing open XML file formats. Mol Syst Biol 1.
    • (2005) Mol Syst Biol , pp. 1
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4    Aebersold, R.5
  • 15
    • 38649129079 scopus 로고    scopus 로고
    • Posterior error probabilities and false discovery rates: Two sides of the same coin
    • Käll L, Storey JD, MacCoss MJ, Noble WS (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res 7: 40-44.
    • (2008) J Proteome Res , vol.7 , pp. 40-44
    • Käll, L.1    Storey, J.D.2    Maccoss, M.J.3    Noble, W.S.4
  • 16
    • 80054038843 scopus 로고    scopus 로고
    • Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment
    • Zhou H, Low TY, Hennrich ML, van der Toorn H, Schwend T, et al. (2011) Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics 10.
    • (2011) Mol Cell Proteomics , pp. 10
    • Zhou, H.1    Low, T.Y.2    Hennrich, M.L.3    Van der Toorn, H.4    Schwend, T.5
  • 17
    • 84859977154 scopus 로고    scopus 로고
    • Phosphoproteome profile of Fusarium graminearum grown in vitro under nonlimiting conditions
    • Rampitsch C, Tinker NA, Subramaniam R, Barkow-Oesterreicher S, Laczko E (2012) Phosphoproteome profile of Fusarium graminearum grown in vitro under nonlimiting conditions. Proteomics 12: 1002-1005.
    • (2012) Proteomics , vol.12 , pp. 1002-1005
    • Rampitsch, C.1    Tinker, N.A.2    Subramaniam, R.3    Barkow-Oesterreicher, S.4    Laczko, E.5
  • 18
    • 82755163993 scopus 로고    scopus 로고
    • Multidimensional strategy for sensitive phosphoproteomics incorporating protein prefractionation combined with SIMAC, HILIC, and TiO(2) chromatography applied to proximal EGF signaling
    • Engholm-Keller K, Hansen TA, Palmisano G, Larsen MR (2011) Multidimensional strategy for sensitive phosphoproteomics incorporating protein prefractionation combined with SIMAC, HILIC, and TiO(2) chromatography applied to proximal EGF signaling. J Proteome Res 10: 5383-5397.
    • (2011) J Proteome Res , vol.10 , pp. 5383-5397
    • Engholm-Keller, K.1    Hansen, T.A.2    Palmisano, G.3    Larsen, M.R.4
  • 19
    • 79960181605 scopus 로고    scopus 로고
    • Modification Site Localization Scoring Integrated into a Search Engine
    • Baker PR, Trinidad JC, Chalkley RJ (2011) Modification Site Localization Scoring Integrated into a Search Engine. Mol Cell Proteomics 10.
    • (2011) Mol Cell Proteomics , pp. 10
    • Baker, P.R.1    Trinidad, J.C.2    Chalkley, R.J.3
  • 20
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean B, Eng JK, Beavis RC, McIntosh M (2006) General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22: 2830-2832.
    • (2006) Bioinformatics , vol.22 , pp. 2830-2832
    • Maclean, B.1    Eng, J.K.2    Beavis, R.C.3    McIntosh, M.4
  • 22
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75.
    • (2012) Nucleic Acids Res , vol.40
  • 23
    • 63049120802 scopus 로고    scopus 로고
    • Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins
    • Cockman ME, Webb JD, Kramer HB, Kessler BM, Ratcliffe PJ (2009) Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins. Mol Cell Proteomics 8: 535-546.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 535-546
    • Cockman, M.E.1    Webb, J.D.2    Kramer, H.B.3    Kessler, B.M.4    Ratcliffe, P.J.5
  • 24
    • 79952858715 scopus 로고    scopus 로고
    • Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains
    • Yang M, Chowdhury R, Ge W, Hamed RB, McDonough MA, et al. (2011) Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains. FEBS J 278: 1086-1097.
    • (2011) FEBS J , vol.278 , pp. 1086-1097
    • Yang, M.1    Chowdhury, R.2    Ge, W.3    Hamed, R.B.4    McDonough, M.A.5
  • 25
    • 79953180051 scopus 로고    scopus 로고
    • Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor
    • Yang M, Ge W, Chowdhury R, Claridge TD, Kramer HB, et al. (2011) Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor. J Biol Chem 286: 7648-7660.
    • (2011) J Biol Chem , vol.286 , pp. 7648-7660
    • Yang, M.1    Ge, W.2    Chowdhury, R.3    Claridge, T.D.4    Kramer, H.B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.