메뉴 건너뛰기




Volumn 75, Issue 1, 2011, Pages 122-126

SPIRE: Systematic protein investigative research environment

Author keywords

Data analysis; Data integration; False discovery rates; Protein annotation; Protein identification; Proteomics pipeline

Indexed keywords

MITOCHONDRIAL PROTEIN; CAENORHABDITIS ELEGANS PROTEIN;

EID: 84858743300     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.05.009     Document Type: Article
Times cited : (24)

References (26)
  • 1
    • 84858720250 scopus 로고    scopus 로고
    • Facing challenges in Proteomics today and the coming decade: Report of Roundtable Discussions at the EuPA Scientific Meeting
    • May 3. [Epub ahead of print].
    • Cox J, M A Heeren R, James P, Jorrin-Novo JV, Kolker E, Levander F, et al. Facing challenges in Proteomics today and the coming decade: Report of Roundtable Discussions at the EuPA Scientific Meeting - Estoril J Proteomics. 2011 May 3. [Epub ahead of print].
    • (2011) Estoril J Proteomics
    • Cox, J.1    M A Heeren, R.2    James, P.3    Jorrin-Novo, J.V.4    Kolker, E.5    Levander, F.6
  • 2
    • 43349084908 scopus 로고    scopus 로고
    • A note on the false discovery rate and inconsistent comparisons between experiments
    • Higdon R., van Belle G., Kolker E. A note on the false discovery rate and inconsistent comparisons between experiments. Bioinformatics 2008, 24:1225-1228.
    • (2008) Bioinformatics , vol.24 , pp. 1225-1228
    • Higdon, R.1    van Belle, G.2    Kolker, E.3
  • 4
    • 77953861977 scopus 로고    scopus 로고
    • Estimating false discovery rates for peptide and protein identification using randomized databases
    • Hather G., Higdon R., Bauman A., von Haller P.D., Kolker E. Estimating false discovery rates for peptide and protein identification using randomized databases. Proteomics 2010, 10:2369-2373.
    • (2010) Proteomics , vol.10 , pp. 2369-2373
    • Hather, G.1    Higdon, R.2    Bauman, A.3    von Haller, P.D.4    Kolker, E.5
  • 5
    • 37349003083 scopus 로고    scopus 로고
    • Experiment-specific estimation of peptide identification probabilities using a randomized database
    • Higdon R., Hogan J.M., Kolker N., van Belle G., Kolker E. Experiment-specific estimation of peptide identification probabilities using a randomized database. OMICS 2007, 11:351-365.
    • (2007) OMICS , vol.11 , pp. 351-365
    • Higdon, R.1    Hogan, J.M.2    Kolker, N.3    van Belle, G.4    Kolker, E.5
  • 6
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 8
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H., Deutsch E.W., Eddes J.S., Eng J.K., King N., Stein S.E., et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 2007, 7:655-667.
    • (2007) Proteomics , vol.7 , pp. 655-667
    • Lam, H.1    Deutsch, E.W.2    Eddes, J.S.3    Eng, J.K.4    King, N.5    Stein, S.E.6
  • 9
    • 33847252600 scopus 로고    scopus 로고
    • A predictive model for identifying proteins by a single peptide match
    • Higdon R., Kolker E. A predictive model for identifying proteins by a single peptide match. Bioinformatics (Oxford, England) 2007, 23:277-280.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , pp. 277-280
    • Higdon, R.1    Kolker, E.2
  • 10
    • 72149093828 scopus 로고    scopus 로고
    • Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
    • Reiter L., Claassen M., Schrimpf S.P., Jovanovic M., Schmidt A., Buhmann J.M., et al. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics 2009, 8:2405-2417.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2405-2417
    • Reiter, L.1    Claassen, M.2    Schrimpf, S.P.3    Jovanovic, M.4    Schmidt, A.5    Buhmann, J.M.6
  • 11
    • 84858713354 scopus 로고    scopus 로고
    • IPM An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics
    • In Press.
    • Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, et al. IPM An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. J Proteomics In Press.
    • J Proteomics
    • Higdon, R.1    Reiter, L.2    Hather, G.3    Haynes, W.4    Kolker, N.5    Stewart, E.6
  • 12
    • 78651319979 scopus 로고    scopus 로고
    • UniProt Consortium: ongoing and future developments at the Universal Protein Resource
    • UniProt Consortium: ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, 39:D214-D219.
    • (2011) Nucleic Acids Res , vol.39
  • 14
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 15
    • 38549117301 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi R., Foerster H., Fulcher C.A., Kaipa P., Krummenacker M., Latendresse M., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2008, 36:D623-D631.
    • (2008) Nucleic Acids Res , vol.36
    • Caspi, R.1    Foerster, H.2    Fulcher, C.A.3    Kaipa, P.4    Krummenacker, M.5    Latendresse, M.6
  • 16
    • 0141742293 scopus 로고    scopus 로고
    • PANTHER: a library of protein families and subfamilies indexed by function
    • Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 2003, 13:2129-2141.
    • (2003) Genome Res , vol.13 , pp. 2129-2141
    • Thomas, P.D.1    Campbell, M.J.2    Kejariwal, A.3    Mi, H.4    Karlak, B.5    Daverman, R.6
  • 18
    • 70449552832 scopus 로고    scopus 로고
    • The GAMMER model of sequence similarity, function specificity, and function similarity for protein annotation
    • Louie B., Higdon R., Kolker E. The GAMMER model of sequence similarity, function specificity, and function similarity for protein annotation. Plos One 2009, 4(10):e7546.
    • (2009) Plos One , vol.4 , Issue.10
    • Louie, B.1    Higdon, R.2    Kolker, E.3
  • 21
    • 77954198983 scopus 로고    scopus 로고
    • Meta-analysis for protein identification: a case study on yeast data
    • Higdon R., Haynes W., Kolker E. Meta-analysis for protein identification: a case study on yeast data. OMICS 2010, 14:309-314.
    • (2010) OMICS , vol.14 , pp. 309-314
    • Higdon, R.1    Haynes, W.2    Kolker, E.3
  • 22
    • 79551505442 scopus 로고    scopus 로고
    • Design and initial characterization of the SC-200 proteomics standard
    • Bauman A., Higdon R., Rapson S., Loiue B., Hogan J., Stacy R., et al. Design and initial characterization of the SC-200 proteomics standard. OMICS 2011, 15:73-82.
    • (2011) OMICS , vol.15 , pp. 73-82
    • Bauman, A.1    Higdon, R.2    Rapson, S.3    Loiue, B.4    Hogan, J.5    Stacy, R.6
  • 23
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller A., Nesvizhskii A.I., 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.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 25
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • [Article 3]
    • Smyth G.K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3. [Article 3].
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 26
    • 35649021196 scopus 로고    scopus 로고
    • Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression
    • Kolker E., Hogan J.M., Higdon R., Kolker N., Landorf E., Yakunin A.F., et al. Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression. Proteomics 2007, 7:3693-3698.
    • (2007) Proteomics , vol.7 , pp. 3693-3698
    • Kolker, E.1    Hogan, J.M.2    Higdon, R.3    Kolker, N.4    Landorf, E.5    Yakunin, A.F.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.