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Volumn 33, Issue 1, 2008, Pages 18-25

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; DATA ANALYSIS; INFORMATION PROCESSING; INFORMATION SYSTEM; INTERNET; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; TANDEM MASS SPECTROMETRY; VALIDATION PROCESS;

EID: 41349096900     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00298.2007     Document Type: Review
Times cited : (129)

References (63)
  • 3
    • 85142204881 scopus 로고    scopus 로고
    • Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22: 1902-1909, 2006.
    • Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin C, Chen J, Goodlett D, Whiteaker J, Paulovich A, McIntosh M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22: 1902-1909, 2006.
  • 5
    • 0141955057 scopus 로고    scopus 로고
    • A method for reducing the time required to match protein sequences with tandem mass spectra
    • Craig R, Beavis RC. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun Mass Spectrom 17: 2310-2316, 2003.
    • (2003) Rapid Commun Mass Spectrom , vol.17 , pp. 2310-2316
    • Craig, R.1    Beavis, R.C.2
  • 6
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • Craig R, Cortens JC, Fenyo D, Beavis RC. Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 5: 1843-1849, 2006.
    • (2006) J Proteome Res , vol.5 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 7
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig R, Cortens JP, Beavis RC. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res 3: 1234-1242, 2004.
    • (2004) J Proteome Res , vol.3 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 12
    • 41349107126 scopus 로고    scopus 로고
    • Distiller. http://www.matrixscience.com/distiller.html.
    • Distiller
  • 13
    • 33750622611 scopus 로고    scopus 로고
    • Challenges and opportunities in proteomics data analysis
    • Domon B, Aebersold R. Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics 5: 1921-1926, 2006.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1921-1926
    • Domon, B.1    Aebersold, R.2
  • 14
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon B, Aebersold R. Mass spectrometry and protein analysis. Science 312: 212-217, 2006.
    • (2006) Science , vol.312 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 15
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214, 2007.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 16
    • 41349091588 scopus 로고    scopus 로고
    • Elucidator. http://rosettabio.com/products/elucidator/default.htm.
    • Elucidator
  • 17
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng J, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989, 1994.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.1    McCormack, A.L.2    Yates, J.R.3
  • 18
    • 41349094093 scopus 로고    scopus 로고
    • Tranche: Secure decentralized data storage for the proteomics community
    • Falkner JA, Andrews PC. Tranche: secure decentralized data storage for the proteomics community. J Biomol Techniques 18: 3, 2007.
    • (2007) J Biomol Techniques , vol.18 , pp. 3
    • Falkner, J.A.1    Andrews, P.C.2
  • 19
    • 33747626954 scopus 로고    scopus 로고
    • Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
    • Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 78: 5678-5684, 2006.
    • (2006) Anal Chem , vol.78 , pp. 5678-5684
    • Frewen, B.E.1    Merrihew, G.E.2    Wu, C.C.3    Noble, W.S.4    MacCoss, M.J.5
  • 23
    • 33750615386 scopus 로고    scopus 로고
    • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5: 1927-1941, 2006.
    • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5: 1927-1941, 2006.
  • 25
    • 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 1: 2005.0017, 2005.
    • 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 1: 2005.0017, 2005.
  • 26
    • 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 AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392, 2002.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 28
    • 33947366516 scopus 로고    scopus 로고
    • Development and validation of a spectral library searching method for peptide identification from MS/MS
    • Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7: 655-667, 2007.
    • (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    Aebersold, R.7
  • 29
    • 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, Garden P, James P, Hakkinen J. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics 7: 668-674, 2007.
    • (2007) Proteomics , vol.7 , pp. 668-674
    • Levander, F.1    Krogh, M.2    Warell, K.3    Garden, P.4    James, P.5    Hakkinen, J.6
  • 30
    • 26844492976 scopus 로고    scopus 로고
    • A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry
    • Li XJ, Yi EC, Kemp CJ, Zhang H, Aebersold R. A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol Cell Proteomics 4: 1328-1340, 2005.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1328-1340
    • Li, X.J.1    Yi, E.C.2    Kemp, C.J.3    Zhang, H.4    Aebersold, R.5
  • 31
    • 0344737959 scopus 로고    scopus 로고
    • Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
    • Li XJ, Zhang H, Ranish JA, Aebersold R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem 75: 6648-6657, 2003.
    • (2003) Anal Chem , vol.75 , pp. 6648-6657
    • Li, X.J.1    Zhang, H.2    Ranish, J.A.3    Aebersold, R.4
  • 32
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu H, Sadygov RG, Yates JR 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201, 2004.
    • (2004) Anal Chem , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates 3rd, J.R.3
  • 33
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-124, 2007.
    • (2007) Nat Biotechnol , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 34
    • 34447313945 scopus 로고    scopus 로고
    • How do shotgun proteomics algorithms identify proteins?
    • Marcotte EM. How do shotgun proteomics algorithms identify proteins? Nat Biotechnol 25: 755-757, 2007.
    • (2007) Nat Biotechnol , vol.25 , pp. 755-757
    • Marcotte, E.M.1
  • 37
    • 41349089337 scopus 로고    scopus 로고
    • Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry
    • December 27, doi:10.1152/ physiolgenomics.00292
    • Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics (December 27, 2007). doi:10.1152/ physiolgenomics.00292.2007.
    • (2007) Physiol Genomics
    • Mirza, S.P.1    Olivier, M.2
  • 38
    • 41349100170 scopus 로고    scopus 로고
    • mzData. http://psidev.info/index.php?q=node/80#mzdata.
    • mzData. http://psidev.info/index.php?q=node/80#mzdata.
  • 39
    • 41349098948 scopus 로고    scopus 로고
    • mzML. http://psidev.info/index.php?q=node/257.
    • mzML. http://psidev.info/index.php?q=node/257.
  • 40
    • 41349111005 scopus 로고    scopus 로고
    • mzXML. http://tools.proteomecenter.org/wiki/index.php?title= Formats:mzXML.
    • mzXML. http://tools.proteomecenter.org/wiki/index.php?title= Formats:mzXML.
  • 41
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75: 4646-4658, 2003.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 42
    • 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 4:787-797, 2007.
    • (2007) Nat Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 43
    • 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, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386, 2002.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 44
    • 34250372908 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture for quantitative proteomics
    • Ong SE, Mann M. Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol 359: 37-52, 2007.
    • (2007) Methods Mol Biol , vol.359 , pp. 37-52
    • Ong, S.E.1    Mann, M.2
  • 45
    • 12944269065 scopus 로고
    • Rapid identification of proteins by peptide-mass fingerprinting
    • Pappin DJ, Hojrup P, Bleasby AJ. Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3: 327-332, 1993.
    • (1993) Curr Biol , vol.3 , pp. 327-332
    • Pappin, D.J.1    Hojrup, P.2    Bleasby, A.J.3
  • 48
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567, 1999.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 49
    • 41349112028 scopus 로고    scopus 로고
    • PFW. Protein Function Workbench. http://db.systemsbiology.net: 8070/fewb/.
    • PFW. Protein Function Workbench. http://db.systemsbiology.net: 8070/fewb/.
  • 50
    • 36248970413 scopus 로고    scopus 로고
    • Sharing detailed research data is associated with increased citation rate
    • Piwowar HA, Day RS, Fridsma DB. Sharing detailed research data is associated with increased citation rate. PLoS ONE 2: e308, 2007.
    • (2007) PLoS ONE , vol.2
    • Piwowar, H.A.1    Day, R.S.2    Fridsma, D.B.3
  • 52
    • 41349107941 scopus 로고    scopus 로고
    • Proteus. http://www.genologics.com/.
    • Proteus
  • 53
    • 30744438115 scopus 로고    scopus 로고
    • Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res 5: 112-121, 2006.
    • Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res 5: 112-121, 2006.
  • 55
    • 33646743767 scopus 로고    scopus 로고
    • The Gaggle: An open-source software system for integrating bioinformatics software and data sources
    • Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 7: 176, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 176
    • Shannon, P.T.1    Reiss, D.J.2    Bonneau, R.3    Baliga, N.S.4
  • 58
    • 0037163144 scopus 로고    scopus 로고
    • Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M. Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A. Design and implementation of Microarray Gene Expression Markup Language (MAGE-ML). Genome Biol 3: RESEARCH0046, 2002.
    • Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M. Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A. Design and implementation of Microarray Gene Expression Markup Language (MAGE-ML). Genome Biol 3: RESEARCH0046, 2002.
  • 62
    • 33751077285 scopus 로고    scopus 로고
    • MASCOT HTML and XML parser: An implementation of a novel object model for protein identification data
    • Yang CG, Granite SJ, Van Eyk JE, Winslow RL. MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data. Proteomics 6: 5688-5693, 2006.
    • (2006) Proteomics , vol.6 , pp. 5688-5693
    • Yang, C.G.1    Granite, S.J.2    Van Eyk, J.E.3    Winslow, R.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.