메뉴 건너뛰기




Volumn 11, Issue 6, 2011, Pages 1172-1180

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods

Author keywords

Bioinformatics; Intensity normalization; Peptide fragmentation; Peptide identification

Indexed keywords

METHANEARSONATE DISODIUM; PEPTIDE FRAGMENT; PEPTIDES AND PROTEINS;

EID: 79952308634     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000605     Document Type: Article
Times cited : (6)

References (36)
  • 1
    • 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
  • 2
    • 84987419408 scopus 로고
    • Proposal for a common nomenclature for sequence ions in mass spectra of peptides
    • Roepstorff, P., Fohlman, J., Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 1984, 11, 601.
    • (1984) Biomed. Mass Spectrom. , vol.11 , pp. 601
    • Roepstorff, P.1    Fohlman, J.2
  • 3
    • 0023449998 scopus 로고
    • Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine
    • Johnson, R. S., Martin, S. A., Biemann, K., Stults, J. T., Watson, J. T., Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Anal. Chem. 1987, 59, 2621-2625.
    • (1987) Anal. Chem. , vol.59 , pp. 2621-2625
    • Johnson, R.S.1    Martin, S.A.2    Biemann, K.3    Stults, J.T.4    Watson, J.T.5
  • 4
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: the protein inference problem
    • Nesvizhskii, A. I., Aebersold, R., Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 2005, 4, 1419-1440.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 5
    • 70349091863 scopus 로고    scopus 로고
    • A guide to the proteomics identifications database proteomics data repository
    • Vizcaíno, J. A., Côté, R., Reisinger, F., Foster, J. M. et al., A guide to the proteomics identifications database proteomics data repository. Proteomics 2009, 9, 4276-4283.
    • (2009) Proteomics , vol.9 , pp. 4276-4283
    • Vizcaíno, J.A.1    Côté, R.2    Reisinger, F.3    Foster, J.M.4
  • 6
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
    • (2004) J. Proteome Res. , vol.3 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 8
    • 66749169317 scopus 로고    scopus 로고
    • Predicting intensity ranks of peptide fragment ions research articles
    • Frank, A. M., Predicting intensity ranks of peptide fragment ions research articles. J. Proteome Res. 2009, 2226-2240.
    • (2009) J. Proteome Res. , pp. 2226-2240
    • Frank, A.M.1
  • 9
    • 0742305695 scopus 로고    scopus 로고
    • Intensity-based protein identification by machine learning from a library of tandem mass spectra
    • Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., Gygi, S. P., Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 2004, 22, 214-219.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 214-219
    • Elias, J.E.1    Gibbons, F.D.2    King, O.D.3    Roth, F.P.4    Gygi, S.P.5
  • 10
    • 46249088907 scopus 로고    scopus 로고
    • Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification
    • Klammer, A. A., Reynolds, S. M., Bilmes, J. A., Maccoss, M. J., Noble, W. S., Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics 2008, 24, 348-356.
    • (2008) Bioinformatics , vol.24 , pp. 348-356
    • Klammer, A.A.1    Reynolds, S.M.2    Bilmes, J.A.3    Maccoss, M.J.4    Noble, W.S.5
  • 11
    • 30744444934 scopus 로고    scopus 로고
    • PepHMM: a hidden Markov model based scoring function for mass spectrometry database search
    • Wan, Y., Yang, A., Chen, T., PepHMM: a hidden Markov model based scoring function for mass spectrometry database search. Anal. Chem. 2006, 78, 432-437.
    • (2006) Anal. Chem. , vol.78 , pp. 432-437
    • Wan, Y.1    Yang, A.2    Chen, T.3
  • 12
    • 0037317111 scopus 로고    scopus 로고
    • Intensity-based statistical scorer for tandem mass spectrometry
    • Havilio, M., Haddad, Y., Similansky, Z., Intensity-based statistical scorer for tandem mass spectrometry. Anal. Chem 2003, 75, 435-444.
    • (2003) Anal. Chem , vol.75 , pp. 435-444
    • Havilio, M.1    Haddad, Y.2    Similansky, Z.3
  • 13
    • 35349021975 scopus 로고    scopus 로고
    • Peptide fragment intensity statistical modeling
    • Colinge, J., Peptide fragment intensity statistical modeling. Anal. Chem. 2007, 79, 7286-7290.
    • (2007) Anal. Chem. , vol.79 , pp. 7286-7290
    • Colinge, J.1
  • 14
    • 51249111303 scopus 로고    scopus 로고
    • A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
    • Zhou, C., Bowler, L. D., Feng, J., A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data. BMC Bioinformatics 2008, 17.
    • (2008) BMC Bioinformatics , vol.17
    • Zhou, C.1    Bowler, L.D.2    Feng, J.3
  • 15
    • 33845453748 scopus 로고    scopus 로고
    • Quality assessment of tandem mass spectra based on cumulative intensity normalization
    • Na, S., Paek, E., Quality assessment of tandem mass spectra based on cumulative intensity normalization. J. Proteome Res. 2006, 5, 3241-3248.
    • (2006) J. Proteome Res. , vol.5 , pp. 3241-3248
    • Na, S.1    Paek, E.2
  • 16
    • 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, A. I., Roos, F. F., Grossmann, J., Vogelzang, M. 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, 652-670.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 652-670
    • Nesvizhskii, A.I.1    Roos, F.F.2    Grossmann, J.3    Vogelzang, M.4
  • 17
    • 24744455665 scopus 로고    scopus 로고
    • Automatic quality assessment of peptide tandem mass spectra
    • Bern, M., Goldberg, D., McDonald, W. H., Yates, J. R., Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2004, 20, i49-i54.
    • (2004) Bioinformatics , vol.20
    • Bern, M.1    Goldberg, D.2    Mcdonald, W.H.3    Yates, J.R.4
  • 18
    • 33847654762 scopus 로고    scopus 로고
    • msmsEval: tandem mass spectral quality assignment for high-throughput proteomics
    • Wong, J. W. H., Sullivan, M. J., Cartwright, H. M., Cagney, G., 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.H.1    Sullivan, M.J.2    Cartwright, H.M.3    Cagney, G.4
  • 19
    • 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., Gevaert, K., Eidhammer, I., Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 2006, 6, 2086-2094.
    • (2006) Proteomics , vol.6 , pp. 2086-2094
    • Flikka, K.1    Martens, L.2    Vandekerckhove, J.3    Gevaert, K.4    Eidhammer, I.5
  • 20
    • 1842580753 scopus 로고    scopus 로고
    • Improving large-scale proteomics by clustering of mass spectrometry data
    • Beer, I., Barnea, E., Ziv, T., Admon, A., Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 2004, 4, 950-960.
    • (2004) Proteomics , vol.4 , pp. 950-960
    • Beer, I.1    Barnea, E.2    Ziv, T.3    Admon, A.4
  • 21
    • 34948824011 scopus 로고    scopus 로고
    • Implementation and application of a versatile clustering tool for tandem mass spectrometry data
    • Flikka, K., Meukens, J., Helsens, K., Vandekerckhove, J. et al., Implementation and application of a versatile clustering tool for tandem mass spectrometry data. Proteomics 2007, 7, 3245-3258.
    • (2007) Proteomics , vol.7 , pp. 3245-3258
    • Flikka, K.1    Meukens, J.2    Helsens, K.3    Vandekerckhove, J.4
  • 22
    • 0037953090 scopus 로고    scopus 로고
    • Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility
    • Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., Yates, J. R., Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 2003, 75, 2470-2477.
    • (2003) Anal. Chem. , vol.75 , pp. 2470-2477
    • Tabb, D.L.1    Maccoss, M.J.2    Wu, C.C.3    Anderson, S.D.4    Yates, J.R.5
  • 24
    • 38649109810 scopus 로고    scopus 로고
    • Clustering millions of tandem mass spectra research articles
    • Frank, A. M., Bandeira, N., Shen, Z., Tanner, S. et al., Clustering millions of tandem mass spectra research articles. J. Proteome Res. 2008, 113-122.
    • (2008) J. Proteome Res. , pp. 113-122
    • Frank, A.M.1    Bandeira, N.2    Shen, Z.3    Tanner, S.4
  • 25
    • 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. 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
  • 26
    • 34447637634 scopus 로고    scopus 로고
    • ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites
    • Hummel, J., Niemann, M., Wienkoop, S., Schulze, W. et al., ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics 2007, 8, 216.
    • (2007) BMC Bioinformatics , vol.8 , pp. 216
    • Hummel, J.1    Niemann, M.2    Wienkoop, S.3    Schulze, W.4
  • 27
    • 33747626954 scopus 로고    scopus 로고
    • Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries
    • Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., MacCoss, M. J., Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 2006, 78, 5678-5684.
    • (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
  • 28
    • 66149152717 scopus 로고    scopus 로고
    • A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins
    • Yen, C., Meyer-Arendt, K., Eichelberger, B., Sun, S. et al., A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol. Cell. Proteomics 2009, 8, 857-869.
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 857-869
    • Yen, C.1    Meyer-Arendt, K.2    Eichelberger, B.3    Sun, S.4
  • 29
    • 70349125897 scopus 로고    scopus 로고
    • X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry
    • Mylonas, R., Mauron, Y., Masselot, A., Binz, P. et al., X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal. Chem. 2009, 81, 7604-7610.
    • (2009) Anal. Chem. , vol.81 , pp. 7604-7610
    • Mylonas, R.1    Mauron, Y.2    Masselot, A.3    Binz, P.4
  • 30
    • 70350449457 scopus 로고    scopus 로고
    • When less can yield more - computational preprocessing of MS/MS spectra for peptide identification
    • Renard, B. Y., Kirchner, M., Monigatti, F., Ivanov, A. R. et al., When less can yield more - computational preprocessing of MS/MS spectra for peptide identification. Proteomics 2009, 9, 4978-4984.
    • (2009) Proteomics , vol.9 , pp. 4978-4984
    • Renard, B.Y.1    Kirchner, M.2    Monigatti, F.3    Ivanov, A.R.4
  • 31
    • 77949750038 scopus 로고    scopus 로고
    • ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
    • Helsens, K., Colaert, N., Barsnes, H., Muth, T. et al., ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics 2010, 10, 1261-1264.
    • (2010) Proteomics , vol.10 , pp. 1261-1264
    • Helsens, K.1    Colaert, N.2    Barsnes, H.3    Muth, T.4
  • 32
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 2003, 21, 566-569.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4
  • 33
    • 42049084149 scopus 로고    scopus 로고
    • Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
    • Staes, A., Van Damme, P., Helsens, K., Demol, H. et al., Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 2008, 8, 1362-1370.
    • (2008) Proteomics , vol.8 , pp. 1362-1370
    • Staes, A.1    Van Damme, P.2    Helsens, K.3    Demol, H.4
  • 34
    • 76749122411 scopus 로고    scopus 로고
    • Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses
    • Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V. et al., Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 2010, 9, 225-241.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 225-241
    • Rudnick, P.A.1    Clauser, K.R.2    Kilpatrick, L.E.3    Tchekhovskoi, D.V.4
  • 35
    • 73649131275 scopus 로고    scopus 로고
    • MSQuant, an open source platform for mass spectrometry-based quantitative proteomics
    • Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S. et al., MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J. Proteome Res. 2010, 9, 393-403.
    • (2010) J. Proteome Res. , vol.9 , pp. 393-403
    • Mortensen, P.1    Gouw, J.W.2    Olsen, J.V.3    Ong, S.4
  • 36
    • 77649120044 scopus 로고    scopus 로고
    • Fragmentation Analyzer: an open-source tool to analyze MS/MS fragmentation data
    • Barsnes, H., Eidhammer, I., Martens, L., Fragmentation Analyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics 2010, 1087-1090.
    • (2010) Proteomics , pp. 1087-1090
    • Barsnes, H.1    Eidhammer, I.2    Martens, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.