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Volumn 9, Issue 2, 2008, Pages 174-188

Information quality in proteomics

Author keywords

Information management; Information quality; Proteomics; Quality assessment; Standards

Indexed keywords

ARTICLE; COMPARATIVE STUDY; COMPLEX FORMATION; COMPUTER PROGRAM; DATA ANALYSIS; EXPERIMENTAL DESIGN; EXPERIMENTAL STUDY; GOOD CLINICAL PRACTICE; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; INFORMATION STORAGE; INTERNET; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRACTICE GUIDELINE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DATABASE; PROTEOMICS; PUBLICATION; QUALITY CONTROL; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 42049089764     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn004     Document Type: Article
Times cited : (30)

References (86)
  • 1
    • 9244226546 scopus 로고    scopus 로고
    • Design and analysis of experiments with high throughput biological assay data
    • Rocke DM. Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 2004; 15:703-13.
    • (2004) Semin Cell Dev Biol , vol.15 , pp. 703-713
    • Rocke, D.M.1
  • 2
    • 33750601062 scopus 로고    scopus 로고
    • The pitfalls of proteomics experiments without the correct use of bioinformatics tools
    • Biron DG, Brun C, Lefevre T, et al. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 2006;6:5577-96.
    • (2006) Proteomics , vol.6 , pp. 5577-5596
    • Biron, D.G.1    Brun, C.2    Lefevre, T.3
  • 3
    • 33750600611 scopus 로고    scopus 로고
    • Proteome informatics I: Bioinformatics tools for processing experimental data
    • Palagi PM, Hernandez P, Walther D, et al. Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 2006;6:5435-44.
    • (2006) Proteomics , vol.6 , pp. 5435-5444
    • Palagi, P.M.1    Hernandez, P.2    Walther, D.3
  • 4
    • 10644230916 scopus 로고    scopus 로고
    • Current two-dimensional electrophoresis technology for proteomics
    • Gorg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics 2004; 4:3665-85.
    • (2004) Proteomics , vol.4 , pp. 3665-3685
    • Gorg, A.1    Weiss, W.2    Dunn, M.J.3
  • 5
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003;422:198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 6
    • 3042735127 scopus 로고    scopus 로고
    • The need for guidelines in publication of peptide and protein identification data
    • Carr S, Aebersold R, Baldwin M, et al. The need for guidelines in publication of peptide and protein identification data. Mol Cell Proteomics 2004;3:531-3.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 531-533
    • Carr, S.1    Aebersold, R.2    Baldwin, M.3
  • 7
    • 27744477157 scopus 로고    scopus 로고
    • Bridging proteomics and systems biology what are the roads to be traveled?
    • Souchelnytskyi S. Bridging proteomics and systems biology what are the roads to be traveled? Proteomics 2005; 5:4123-37.
    • (2005) Proteomics , vol.5 , pp. 4123-4137
    • Souchelnytskyi, S.1
  • 8
    • 35848968214 scopus 로고    scopus 로고
    • The protein microscope: Incorporating mass spectrometry into cell biology
    • Bell AW, Nilsson T, Kearney RE, et al. The protein microscope: incorporating mass spectrometry into cell biology. Nat Methods 2007;4:783-4.
    • (2007) Nat Methods , vol.4 , pp. 783-784
    • Bell, A.W.1    Nilsson, T.2    Kearney, R.E.3
  • 9
    • 33745978799 scopus 로고    scopus 로고
    • Evaluation of two sample preparation methods for prostate proteome analysis
    • Lexander H, Hellman U, Palmberg C, et al. Evaluation of two sample preparation methods for prostate proteome analysis. Proteomics 2006;6:3918-25.
    • (2006) Proteomics , vol.6 , pp. 3918-3925
    • Lexander, H.1    Hellman, U.2    Palmberg, C.3
  • 10
    • 30744440918 scopus 로고    scopus 로고
    • Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: Quantity, quality, and variability
    • Thongboonkerd V, Chutipongtanate S, Kanlaya R. Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability. J Proteome Res 2006;5 183-91.
    • (2006) J Proteome Res , vol.5 , pp. 183-191
    • Thongboonkerd, V.1    Chutipongtanate, S.2    Kanlaya, R.3
  • 11
    • 33846464622 scopus 로고    scopus 로고
    • A standard operating procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis
    • Schwarz K, Fiedler T, Fischer RJ, et al. A standard operating procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis. J Microbiol Methods 2007;68:396-402.
    • (2007) J Microbiol Methods , vol.68 , pp. 396-402
    • Schwarz, K.1    Fiedler, T.2    Fischer, R.J.3
  • 12
    • 20844446602 scopus 로고    scopus 로고
    • Optimal replication and the importance of experimental design for gel-based quantitative proteomics
    • Hunt SM, Thomas MR, Sebastian LT, et al. Optimal replication and the importance of experimental design for gel-based quantitative proteomics. J Proteome Res 2005;4: 809-19.
    • (2005) J Proteome Res , vol.4 , pp. 809-819
    • Hunt, S.M.1    Thomas, M.R.2    Sebastian, L.T.3
  • 13
    • 26844438450 scopus 로고    scopus 로고
    • Impact of replicate types on proteomics expression analysis
    • Karp NA, Spencer M, Lindsay H, et al. Impact of replicate types on proteomics expression analysis. J Proteome Res 2005; 4 1867-71.
    • (2005) J Proteome Res , vol.4 , pp. 1867-1871
    • Karp, N.A.1    Spencer, M.2    Lindsay, H.3
  • 14
    • 0023768475 scopus 로고
    • The current state of two-dimensional electrophoresis with immobilized pH gradients
    • Gorg A, Postel W, Gunther S. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 1988;9:531-46.
    • (1988) Electrophoresis , vol.9 , pp. 531-546
    • Gorg, A.1    Postel, W.2    Gunther, S.3
  • 15
    • 3543118467 scopus 로고    scopus 로고
    • Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae
    • Yin Z, Stead D, Selway L, et al. Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae. Proteomics 2004;4:2425-36.
    • (2004) Proteomics , vol.4 , pp. 2425-2436
    • Yin, Z.1    Stead, D.2    Selway, L.3
  • 16
    • 39049191688 scopus 로고    scopus 로고
    • Quantitative analysis of 2D gels
    • Zivy M. Quantitative analysis of 2D gels. Methods Mol Biol 2007; 355:175-94.
    • (2007) Methods Mol Biol , vol.355 , pp. 175-194
    • Zivy, M.1
  • 17
    • 23844491490 scopus 로고    scopus 로고
    • Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes
    • Karp NA, Lilley KS. Maximising sensitivity for detecting changes in protein expression: Experimental design using minimal CyDyes. Proteomics 2005;5:3105-15.
    • (2005) Proteomics , vol.5 , pp. 3105-3115
    • Karp, N.A.1    Lilley, K.S.2
  • 18
    • 32244443103 scopus 로고    scopus 로고
    • Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis
    • Marengo E, Robotti E, Bobba M, et al. Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis. Electrophoresis 2006;27: 484-94.
    • (2006) Electrophoresis , vol.27 , pp. 484-494
    • Marengo, E.1    Robotti, E.2    Bobba, M.3
  • 20
    • 16344384887 scopus 로고    scopus 로고
    • The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales
    • Hu J, Coombes KR, Morris JS, et al. The importance of experimental design in proteomic mass spectrometry experiments: Some cautionary tales. Brief Funct Genomic Proteomic 2005;3:322-31.
    • (2005) Brief Funct Genomic Proteomic , vol.3 , pp. 322-331
    • Hu, J.1    Coombes, K.R.2    Morris, J.S.3
  • 21
    • 0041884952 scopus 로고    scopus 로고
    • Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to μ LC-ESI tandem mass spectrometry
    • Lim H, Eng J, Yates JR 3rd, et al. Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to μ LC-ESI tandem mass spectrometry. J Am Soc Mass Spectrom 2003;14 957-70.
    • (2003) J Am Soc Mass Spectrom , vol.14 , pp. 957-970
    • Lim, H.1    Eng, J.2    Yates 3rd, J.R.3
  • 22
    • 33746302310 scopus 로고    scopus 로고
    • Universal metrics for quality assessment of protein identifications by mass spectrometry
    • Stead DA, Preece A, Brown AJP. Universal metrics for quality assessment of protein identifications by mass spectrometry. Mol Cell Proteomics 2006;5:1205-11.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1205-1211
    • Stead, D.A.1    Preece, A.2    Brown, A.J.P.3
  • 23
    • 42049116382 scopus 로고    scopus 로고
    • Aldente. http://ca.expasy.org/tools/aldente/ (7 January 2008, date last accessed).
    • Aldente. http://ca.expasy.org/tools/aldente/ (7 January 2008, date last accessed).
  • 25
    • 42049097079 scopus 로고    scopus 로고
    • Mascot. http://www.matrixscience.com/search_forrm_select.html/ (7 January 2008, date last accessed).
    • Mascot. http://www.matrixscience.com/search_forrm_select.html/ (7 January 2008, date last accessed).
  • 26
    • 42049086161 scopus 로고    scopus 로고
    • ProFound. http://prowl.rockefeller.edu/prowl-cgi/profound.exe/ (7 January 2008, date last accessed).
    • ProFound. http://prowl.rockefeller.edu/prowl-cgi/profound.exe/ (7 January 2008, date last accessed).
  • 27
    • 1542720811 scopus 로고    scopus 로고
    • Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data
    • Chamrad DC, Korting G, Stuhler K, et al. Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 2004;4: 619-28.
    • (2004) Proteomics , vol.4 , pp. 619-628
    • Chamrad, D.C.1    Korting, G.2    Stuhler, K.3
  • 29
    • 39049175370 scopus 로고    scopus 로고
    • Protein identification by tandem mass spectrometry and sequence database searching
    • Nesvizhskii AI. Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol Biol 2007;367 87-119.
    • (2007) Methods Mol Biol , vol.367 , pp. 87-119
    • Nesvizhskii, A.I.1
  • 30
    • 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;66:4390-9.
    • (1994) Anal Chem , vol.66 , pp. 4390-4399
    • Mann, M.1    Wilm, M.2
  • 31
    • 42049100616 scopus 로고    scopus 로고
    • SEQUEST. http://fields.scripps.edu/sequest/ (7 January 2008, date last accessed).
    • SEQUEST. http://fields.scripps.edu/sequest/ (7 January 2008, date last accessed).
  • 32
    • 15744400109 scopus 로고    scopus 로고
    • Comparison of different search engines using validated MS/MS test datasets
    • Boutilier K, Ross M, Podtelejnikov AV, et al. Comparison of different search engines using validated MS/MS test datasets. Anal Chim Acta 2005;534:11-20.
    • (2005) Anal Chim Acta , vol.534 , pp. 11-20
    • Boutilier, K.1    Ross, M.2    Podtelejnikov, A.V.3
  • 33
    • 23944451618 scopus 로고    scopus 로고
    • An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS seareh algorithms: Sensitivity and specificity analysis
    • Kapp EA, Schutz F, Connolly LM, et al. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS seareh algorithms: Sensitivity and specificity analysis. Proteomics 2005;5:3475-90.
    • (2005) Proteomics , vol.5 , pp. 3475-3490
    • Kapp, E.A.1    Schutz, F.2    Connolly, L.M.3
  • 34
    • 42049116381 scopus 로고    scopus 로고
    • Phenyx main site. http://www.phenyx-ms.com/ (7 January 2008, date last accessed).
    • Phenyx main site. http://www.phenyx-ms.com/ (7 January 2008, date last accessed).
  • 35
    • 42049114525 scopus 로고    scopus 로고
    • Phenyx public server. http://phenyx.vital-it.ch/pwi/ (7 January 2008, date last accessed).
    • Phenyx public server. http://phenyx.vital-it.ch/pwi/ (7 January 2008, date last accessed).
  • 36
    • 42049088797 scopus 로고    scopus 로고
    • OMSSA. http://pubchem.ncbi.nlm.nih.gov/omssa/ (7 January 2008, date last accessed).
    • OMSSA. http://pubchem.ncbi.nlm.nih.gov/omssa/ (7 January 2008, date last accessed).
  • 37
    • 42049123302 scopus 로고    scopus 로고
    • X! Tandem. http://www.thegpm.org/TANDEM/index.html/ (7 January 2008, date last accessed).
    • X! Tandem. http://www.thegpm.org/TANDEM/index.html/ (7 January 2008, date last accessed).
  • 38
    • 39049191583 scopus 로고    scopus 로고
    • Proteomic data exchange and storage: The need for common standards and public repositories
    • Orchard S, Jones P, Taylor C, et al. Proteomic data exchange and storage: The need for common standards and public repositories. Methods Mol Biol 2007;367:261-70.
    • (2007) Methods Mol Biol , vol.367 , pp. 261-270
    • Orchard, S.1    Jones, P.2    Taylor, C.3
  • 39
    • 24744455665 scopus 로고    scopus 로고
    • Automatic quality assessment of peptide tandem mass spectra
    • Bern M, Goldberg D, McDonald WH, et al. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2004; 20(Suppl 1):I49-54.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Bern, M.1    Goldberg, D.2    McDonald, W.H.3
  • 40
    • 33645653958 scopus 로고    scopus 로고
    • Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
    • Flikka K, Martens L, Vandekerckhove J, et al. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 2006;6: 2086-94.
    • (2006) Proteomics , vol.6 , pp. 2086-2094
    • Flikka, K.1    Martens, L.2    Vandekerckhove, J.3
  • 41
    • 33645708138 scopus 로고    scopus 로고
    • Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
    • Nesvizhskii AI, Roos FF, Grossmann J, et al. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 2006;5:652-70.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.I.1    Roos, F.F.2    Grossmann, J.3
  • 42
    • 33847654762 scopus 로고    scopus 로고
    • msmsEval: Tandem mass spectral quality assignment for high-throughput proteomics
    • Wong JW, Sullivan MJ, Cartwright HM, et al. msmsEval: Tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics 2007;8:51.
    • (2007) BMC Bioinformatics , vol.8 , pp. 51
    • Wong, J.W.1    Sullivan, M.J.2    Cartwright, H.M.3
  • 43
    • 33645467062 scopus 로고    scopus 로고
    • Improved classification of mass spectrometry database search results using newer machine learning approaches
    • Ulintz PJ, Zhu J, Qin ZS, et al. Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics 2006;5:497-509.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 497-509
    • Ulintz, P.J.1    Zhu, J.2    Qin, Z.S.3
  • 44
    • 27944488300 scopus 로고    scopus 로고
    • Confident protein identification using like average peptide score method coupled with search-specific, ab initio thresholds
    • Shadforth I, Dunkley T, Lilley K, et al. Confident protein identification using like average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom 2005;19:3363-8.
    • (2005) Rapid Commun Mass Spectrom , vol.19 , pp. 3363-3368
    • Shadforth, I.1    Dunkley, T.2    Lilley, K.3
  • 45
    • 24044508863 scopus 로고    scopus 로고
    • New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques
    • Savitski MM, Nielsen ML, Zubarev RA. New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol Cell Proteomics 2005; 4 1180-8.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1180-1188
    • Savitski, M.M.1    Nielsen, M.L.2    Zubarev, R.A.3
  • 46
    • 33745828376 scopus 로고    scopus 로고
    • Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles
    • Piening BD, Wang P, Bangur CS, et al. Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles. J Proteome Res 2006;5:1527-34.
    • (2006) J Proteome Res , vol.5 , pp. 1527-1534
    • Piening, B.D.1    Wang, P.2    Bangur, C.S.3
  • 47
    • 42049122886 scopus 로고    scopus 로고
    • Global Proteome Machine. http://gpmdb.thegpm.org/ (7 January 2008, date last accessed).
    • Global Proteome Machine. http://gpmdb.thegpm.org/ (7 January 2008, date last accessed).
  • 48
    • 42049084043 scopus 로고    scopus 로고
    • PeptideAtlas. http://www.peptideatlas.org/ (7 January 2008, date last accessed).
    • PeptideAtlas. http://www.peptideatlas.org/ (7 January 2008, date last accessed).
  • 50
    • 34548802987 scopus 로고    scopus 로고
    • Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/ peptide sequence false match frequencies
    • Feng J, Naiman DQ, Cooper B. Probability-based pattern recognition and statistical framework for randomization: Modeling tandem mass spectrum/ peptide sequence false match frequencies. Bioinformatics 2007; 23:2210-7.
    • (2007) Bioinformatics , vol.23 , pp. 2210-2217
    • Feng, J.1    Naiman, D.Q.2    Cooper, B.3
  • 51
    • 34249316472 scopus 로고    scopus 로고
    • Estimating the statistical significance of peptide identifications from shotgun proteomics experiments
    • Higgs RE, Knierman MD, Freeman AB, et al. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments. J Proteome Res 2007;6: 1758-67.
    • (2007) J Proteome Res , vol.6 , pp. 1758-1767
    • Higgs, R.E.1    Knierman, M.D.2    Freeman, A.B.3
  • 52
    • 33846567441 scopus 로고    scopus 로고
    • Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy
    • Huttlin EL, Hegeman AD, Harms AC, et al. Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. J Proteome Res 2007;6:392-8.
    • (2007) J Proteome Res , vol.6 , pp. 392-398
    • Huttlin, E.L.1    Hegeman, A.D.2    Harms, A.C.3
  • 53
    • 31344448066 scopus 로고    scopus 로고
    • Guidelines for the next 10 years of proteomics
    • Wilkins MR, Appel RD, Van Eyk JE, et al. Guidelines for the next 10 years of proteomics. Proteomics 2006;6:4-8.
    • (2006) Proteomics , vol.6 , pp. 4-8
    • Wilkins, M.R.1    Appel, R.D.2    Van Eyk, J.E.3
  • 54
    • 33644524918 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics turns quantitative
    • Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 2005;1:252-62.
    • (2005) Nat Chem Biol , vol.1 , pp. 252-262
    • Ong, S.E.1    Mann, M.2
  • 55
    • 19444363756 scopus 로고    scopus 로고
    • Mass spectrometry-based quantitative proteomic profiling
    • Yan W, Chen SS. Mass spectrometry-based quantitative proteomic profiling. Brief Funct Genomic Proteomic 2005;4: 27-38.
    • (2005) Brief Funct Genomic Proteomic , vol.4 , pp. 27-38
    • Yan, W.1    Chen, S.S.2
  • 56
    • 33846926966 scopus 로고    scopus 로고
    • Amino acid-coded tagging approaches in quantitative proteomics
    • Chen X, Sun L, Yu Y, et al. Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics 2007;4:25-37.
    • (2007) Expert Rev Proteomics , vol.4 , pp. 25-37
    • Chen, X.1    Sun, L.2    Yu, Y.3
  • 57
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong SE, Blagoev B, Kratchmarova I, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Gell Proteomics 2002;1:376-86.
    • (2002) Mol Gell Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3
  • 58
    • 13244260803 scopus 로고    scopus 로고
    • A novel strategy for quantitative proteomics using isotope-coded protein labels
    • Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005; 5:4-15.
    • (2005) Proteomics , vol.5 , pp. 4-15
    • Schmidt, A.1    Kellermann, J.2    Lottspeich, F.3
  • 59
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3:1154-69.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3
  • 61
    • 20644442887 scopus 로고    scopus 로고
    • MSight: An image analysis software for liquid chromatography-mass spectrometry
    • Palagi PM, Walther D, Quadroni M, et al. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005;5:2381-4.
    • (2005) Proteomics , vol.5 , pp. 2381-2384
    • Palagi, P.M.1    Walther, D.2    Quadroni, M.3
  • 62
    • 42049085346 scopus 로고    scopus 로고
    • MSight. http://www.expasy.org/MSight/ (7 January 2008, date last accessed).
    • MSight. http://www.expasy.org/MSight/ (7 January 2008, date last accessed).
  • 63
    • 33947434519 scopus 로고    scopus 로고
    • Automated reporting from gel-based proteomics experiments using the open source Proteios database application
    • Levander F, Krogh M, Warell K, et al. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 2007;7: 668-74.
    • (2007) Proteomics , vol.7 , pp. 668-674
    • Levander, F.1    Krogh, M.2    Warell, K.3
  • 64
    • 33750601225 scopus 로고    scopus 로고
    • Proteome informatics II: Bioinformatics for comparative proteomics
    • Lisacek F, Cohen-Boulakia S, Appel RD. Proteome informatics II: bioinformatics for comparative proteomics. Proteomics 2006;6 5445-66.
    • (2006) Proteomics , vol.6 , pp. 5445-5466
    • Lisacek, F.1    Cohen-Boulakia, S.2    Appel, R.D.3
  • 65
    • 42049110209 scopus 로고    scopus 로고
    • Trans-Proteomic Pipeline. http://tools.proteomecenter.org/software.php/ (7 January 2008, date last accessed).
    • Trans-Proteomic Pipeline. http://tools.proteomecenter.org/software.php/ (7 January 2008, date last accessed).
  • 66
    • 33746930864 scopus 로고    scopus 로고
    • Keller A, Eng J, Zhang N, Li XJ. Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005;1:2005.0017 [Epub 2005 Aug 2].
    • Keller A, Eng J, Zhang N, Li XJ. Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005;1:2005.0017 [Epub 2005 Aug 2].
  • 67
    • 42049084247 scopus 로고    scopus 로고
    • Proteome Standards Initiative. http://www.psidev.info/ (7 January 2008, date last accessed).
    • Proteome Standards Initiative. http://www.psidev.info/ (7 January 2008, date last accessed).
  • 68
    • 42049094713 scopus 로고    scopus 로고
    • Human Proteome Organisation. http://www.hupo.org/ (7 January 2008, date last accessed).
    • Human Proteome Organisation. http://www.hupo.org/ (7 January 2008, date last accessed).
  • 69
    • 33750285086 scopus 로고    scopus 로고
    • The HUPO proteomics standards initiative - overcoming the fragmentation of proteomics data
    • Hermjakob U. The HUPO proteomics standards initiative - overcoming the fragmentation of proteomics data. Proteomics 2006;6:34-8.
    • (2006) Proteomics , vol.6 , pp. 34-38
    • Hermjakob, U.1
  • 70
    • 34249062964 scopus 로고    scopus 로고
    • The minimum information about a proteomics: Experiment (MIAPE)
    • Taylor CF, Paton NW, Lilley KS, et al. The minimum information about a proteomics: Experiment (MIAPE). Nat Biotechnol 2007;25 887-93.
    • (2007) Nat Biotechnol , vol.25 , pp. 887-893
    • Taylor, C.F.1    Paton, N.W.2    Lilley, K.S.3
  • 71
    • 0742323374 scopus 로고    scopus 로고
    • The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data
    • Hermjakob H, Montecchi-Palazzi L, Bader G, et al. The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat Biotechnol 2004;22:177-83.
    • (2004) Nat Biotechnol , vol.22 , pp. 177-183
    • Hermjakob, H.1    Montecchi-Palazzi, L.2    Bader, G.3
  • 72
    • 0037337307 scopus 로고    scopus 로고
    • A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    • Taylor CF, Paton NW, Garwood KL, et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 2003;21: 247-54.
    • (2003) Nat Biotechnol , vol.21 , pp. 247-254
    • Taylor, C.F.1    Paton, N.W.2    Garwood, K.L.3
  • 73
    • 8344284323 scopus 로고    scopus 로고
    • A common open representation of mass spectrometry data and its application to proteomics research
    • Pedrioli PG, Eng JK, Hubley R, et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 2004;22: 1459-66.
    • (2004) Nat Biotechnol , vol.22 , pp. 1459-1466
    • Pedrioli, P.G.1    Eng, J.K.2    Hubley, R.3
  • 74
    • 9144233086 scopus 로고    scopus 로고
    • PEDRo: A database for storing, searching and disseminating experimental proteomics data
    • Garwood K, McLaughlin T, Garwood C, et al. PEDRo: A database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004;5: 68.
    • (2004) BMC Genomics , vol.5 , pp. 68
    • Garwood, K.1    McLaughlin, T.2    Garwood, C.3
  • 75
    • 42049092194 scopus 로고    scopus 로고
    • PRIDE. http://www.ebi.ac.uk/pride/ (7 January 2008, date last accessed).
    • PRIDE. http://www.ebi.ac.uk/pride/ (7 January 2008, date last accessed).
  • 76
    • 42049087705 scopus 로고    scopus 로고
    • Open Proteomics Database. http://bioinformatics.icmb.utexas.edu/OPD/ (7 January 2008, date last accessed).
    • Open Proteomics Database. http://bioinformatics.icmb.utexas.edu/OPD/ (7 January 2008, date last accessed).
  • 77
    • 42049083408 scopus 로고    scopus 로고
    • Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (7 January 2008, date last accessed).
    • Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (7 January 2008, date last accessed).
  • 78
    • 42049107855 scopus 로고    scopus 로고
    • Proteome Harvest Spreadsheet. http://www.ebi.ac.uk/pride/ proteomeharvest/index.html (7 January 2008, date last accessed).
    • Proteome Harvest Spreadsheet. http://www.ebi.ac.uk/pride/ proteomeharvest/index.html (7 January 2008, date last accessed).
  • 79
    • 23944492134 scopus 로고    scopus 로고
    • Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database
    • Omenn GS, States DJ, Adamski M, et al. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005;5:3226-45.
    • (2005) Proteomics , vol.5 , pp. 3226-3245
    • Omenn, G.S.1    States, D.J.2    Adamski, M.3
  • 80
    • 35648980489 scopus 로고    scopus 로고
    • Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics
    • Prakash A, Piening B, Whiteaker J, et al. Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics 2007;6:1741-8.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1741-1748
    • Prakash, A.1    Piening, B.2    Whiteaker, J.3
  • 81
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007;4:787-97.
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 82
    • 42049099761 scopus 로고    scopus 로고
    • PEDRo Data Collator. http://pedrodownload.man.ac.uk/ (7 January 2008, date last accessed).
    • PEDRo Data Collator. http://pedrodownload.man.ac.uk/ (7 January 2008, date last accessed).
  • 84
    • 42049104427 scopus 로고    scopus 로고
    • Qurator. http://www.qurator.org/ (7 January 2008, date last accessed).
    • Qurator. http://www.qurator.org/ (7 January 2008, date last accessed).
  • 85
    • 42049088361 scopus 로고    scopus 로고
    • Taverna. http://taverna.sourceforge.net/ (7 January 2008, date last accessed).
    • Taverna. http://taverna.sourceforge.net/ (7 January 2008, date last accessed).


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