메뉴 건너뛰기




Volumn 15, Issue 5-6, 2015, Pages 930-950

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

Author keywords

Bioinformatics; Databases; MS; Repositories

Indexed keywords

CARDIAC ORGANELLAR PROTEIN ATLAS KNOWLEDGEBASE; CHORUS DATABASE; CLINICAL DATA REPOSITORY; DATA BASE; DATA MINING; GLOBAL PROTEOME MACHINE DATABASE; HUMAN PROTEINPEDIA DATABASE; HUMAN PROTEOME MAP DATABASE; IPROX DATABASE; MASS SPECTROMETRY INTERACTIVE VIRTUAL ENVIRONMENT DATA REPOSITORY; MAXQB DATABASE; MODEL ORGANISM PROTEIN EXPRESSION DATABASE; NEXTPROT DATABASE; PAXDB DATABASE; PEP2PRO DATABASE; PEPTIDEATLAS DATABASE; PEPTIDEATLAS SRM EXPERIMENT LIBRARY DATABASE; PRIDE DATABASE; PRIORITY JOURNAL; PROTEOMICS; PROTEOMICSDB DATABASE; REVIEW; UNIPROT DATABASE; MASS SPECTROMETRY; PROTEIN DATABASE;

EID: 84920070787     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400302     Document Type: Review
Times cited : (156)

References (141)
  • 1
    • 84871297843 scopus 로고    scopus 로고
    • Next-generation proteomics: towards an integrative view of proteome dynamics
    • Altelaar, A. F., Munoz, J., Heck, A. J., Next-generation proteomics: towards an integrative view of proteome dynamics. Nat. Rev. Genet. 2013, 14, 35-48.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 35-48
    • Altelaar, A.F.1    Munoz, J.2    Heck, A.J.3
  • 2
    • 84881487283 scopus 로고    scopus 로고
    • SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping
    • Betancourt, L. H., De Bock, P. J., Staes, A., Timmerman, E. et al., SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping. J. Proteomics 2013, 91, 164-171.
    • (2013) J. Proteomics , vol.91 , pp. 164-171
    • Betancourt, L.H.1    De Bock, P.J.2    Staes, A.3    Timmerman, E.4
  • 3
    • 84894619287 scopus 로고    scopus 로고
    • HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
    • Branca, R. M., Orre, L. M., Johansson, H. J., Granholm, V. et al., HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat. Methods 2014, 11, 59-62.
    • (2014) Nat. Methods , vol.11 , pp. 59-62
    • Branca, R.M.1    Orre, L.M.2    Johansson, H.J.3    Granholm, V.4
  • 4
    • 49849106361 scopus 로고    scopus 로고
    • Proteomics based on peptide fractionation by SDS-free PAGE
    • Ramos, Y., Gutierrez, E., Machado, Y., Sanchez, A. et al., Proteomics based on peptide fractionation by SDS-free PAGE. J. Proteome Res. 2008, 7, 2427-2434.
    • (2008) J. Proteome Res. , vol.7 , pp. 2427-2434
    • Ramos, Y.1    Gutierrez, E.2    Machado, Y.3    Sanchez, A.4
  • 5
    • 79956021267 scopus 로고    scopus 로고
    • Peptide fractionation by acid pH SDS-free electrophoresis
    • Ramos, Y., Garcia, Y., Perez-Riverol, Y., Leyva, A. et al., Peptide fractionation by acid pH SDS-free electrophoresis. Electrophoresis 2011, 32, 1323-1326.
    • (2011) Electrophoresis , vol.32 , pp. 1323-1326
    • Ramos, Y.1    Garcia, Y.2    Perez-Riverol, Y.3    Leyva, A.4
  • 6
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski, J. R., Zougman, A., Nagaraj, N., Mann, M., Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
    • (2009) Nat. Methods , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 7
    • 80052769923 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
    • M111 011015
    • Michalski, A., Damoc, E., Hauschild, J. P., Lange, O. et al., Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 2011, 10, M111 011015.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Michalski, A.1    Damoc, E.2    Hauschild, J.P.3    Lange, O.4
  • 8
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • UniProt, C., Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucl. Acids Res. 2013, 41, D43-D47.
    • (2013) Nucl. Acids Res. , vol.41 , pp. D43-D47
    • UniProt, C.1
  • 9
    • 84890425321 scopus 로고    scopus 로고
    • Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective
    • Perez-Riverol, Y., Wang, R., Hermjakob, H., Muller, M. et al., Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim. Biophys. Acta 2014, 1844, 63-76.
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 63-76
    • Perez-Riverol, Y.1    Wang, R.2    Hermjakob, H.3    Muller, M.4
  • 11
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J. et al., Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 2011, 7, 548.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 548
    • Nagaraj, N.1    Wisniewski, J.R.2    Geiger, T.3    Cox, J.4
  • 12
    • 84864031015 scopus 로고    scopus 로고
    • PRIDE: quality control in a proteomics data repository
    • bas004
    • Csordas, A., Ovelleiro, D., Wang, R., Foster, J. M. et al., PRIDE: quality control in a proteomics data repository. Database 2012, 2012, bas004.
    • (2012) Database , vol.2012
    • Csordas, A.1    Ovelleiro, D.2    Wang, R.3    Foster, J.M.4
  • 13
    • 67650459577 scopus 로고    scopus 로고
    • Credit where credit is overdue
    • Credit where credit is overdue. Nat. Biotechnol. 2009, 27, 579.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 579
  • 14
    • 84890021402 scopus 로고    scopus 로고
    • Mass spectrometry-based quantification
    • DeSouza, L. V., Siu, K. W., Mass spectrometry-based quantification. Clin. Biochem. 2013, 46, 421-431.
    • (2013) Clin. Biochem. , vol.46 , pp. 421-431
    • DeSouza, L.V.1    Siu, K.W.2
  • 15
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: approaches in label-free quantitative mass spectrometry
    • Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3    Mirzaei, M.4
  • 16
    • 80054760698 scopus 로고    scopus 로고
    • Algorithms for the de novo sequencing of peptides from tandem mass spectra
    • Allmer, J., Algorithms for the de novo sequencing of peptides from tandem mass spectra. Expert Rev. Proteomics 2011, 8, 645-657.
    • (2011) Expert Rev. Proteomics , vol.8 , pp. 645-657
    • Allmer, J.1
  • 17
    • 84872272080 scopus 로고    scopus 로고
    • Current algorithmic solutions for peptide-based proteomics data generation and identification
    • Hoopmann, M. R., Moritz, R. L., Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr. Opin. Biotechnol. 2013, 24, 31-38.
    • (2013) Curr. Opin. Biotechnol. , vol.24 , pp. 31-38
    • Hoopmann, M.R.1    Moritz, R.L.2
  • 19
    • 70349912263 scopus 로고    scopus 로고
    • False discovery rates of protein identifications: a strike against the two-peptide rule
    • Gupta, N., Pevzner, P. A., False discovery rates of protein identifications: a strike against the two-peptide rule. J. Proteome Res. 2009, 8, 4173-4181.
    • (2009) J. Proteome Res. , vol.8 , pp. 4173-4181
    • Gupta, N.1    Pevzner, P.A.2
  • 20
    • 84855461974 scopus 로고    scopus 로고
    • Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
    • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. et al., Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics 2012, 12, 11-20.
    • (2012) Proteomics , vol.12 , pp. 11-20
    • Kinsinger, C.R.1    Apffel, J.2    Baker, M.3    Bian, X.4
  • 21
    • 84870806563 scopus 로고    scopus 로고
    • A home for raw proteomics data
    • Anonymous
    • Anonymous, A home for raw proteomics data. Nat. Methods 2012, 9, 419.
    • (2012) Nat. Methods , vol.9 , pp. 419
  • 22
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics
    • Distler, U., Kuharev, J., Navarro, P., Levin, Y. et al., Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat. Methods 2014, 11, 167-170.
    • (2014) Nat. Methods , vol.11 , pp. 167-170
    • Distler, U.1    Kuharev, J.2    Navarro, P.3    Levin, Y.4
  • 23
    • 84896933849 scopus 로고    scopus 로고
    • The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics
    • Lanucara, F., Holman, S. W., Gray, C. J., Eyers, C. E., The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat. Chem. 2014, 6, 281-294.
    • (2014) Nat. Chem. , vol.6 , pp. 281-294
    • Lanucara, F.1    Holman, S.W.2    Gray, C.J.3    Eyers, C.E.4
  • 24
    • 70350217754 scopus 로고    scopus 로고
    • Proteomics data repositories
    • Riffle, M., Eng, J. K., Proteomics data repositories. Proteomics 2009, 9, 4653-4663.
    • (2009) Proteomics , vol.9 , pp. 4653-4663
    • Riffle, M.1    Eng, J.K.2
  • 25
    • 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
  • 26
    • 84891786993 scopus 로고    scopus 로고
    • State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project
    • Farrah, T., Deutsch, E. W., Omenn, G. S., Sun, Z. et al., State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J. Proteome Res. 2014, 13, 60-75.
    • (2014) J. Proteome Res. , vol.13 , pp. 60-75
    • Farrah, T.1    Deutsch, E.W.2    Omenn, G.S.3    Sun, Z.4
  • 27
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
    • Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A. et al., The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucl. Acids Res. 2013, 41, D1063-D1069.
    • (2013) Nucl. Acids Res. , vol.41 , pp. D1063-D1069
    • Vizcaino, J.A.1    Cote, R.G.2    Csordas, A.3    Dianes, J.A.4
  • 28
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M., Schlegl, J., Hahne, H., Moghaddas Gholami, A. et al., Mass-spectrometry-based draft of the human proteome. Nature 2014, 509, 582-587.
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1    Schlegl, J.2    Hahne, H.3    Moghaddas Gholami, A.4
  • 29
    • 84857980282 scopus 로고    scopus 로고
    • Analysis of high accuracy, quantitative proteomics data in the MaxQB database
    • M111014068
    • Schaab, C., Geiger, T., Stoehr, G., Cox, J., Mann, M., Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell. Proteomics 2012, 11, M111.014068.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Schaab, C.1    Geiger, T.2    Stoehr, G.3    Cox, J.4    Mann, M.5
  • 30
    • 84860856503 scopus 로고    scopus 로고
    • PASSEL: the PeptideAtlas SRM experiment library
    • Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z. et al., PASSEL: the PeptideAtlas SRM experiment library. Proteomics 2012, 12, 1170-1175.
    • (2012) Proteomics , vol.12 , pp. 1170-1175
    • Farrah, T.1    Deutsch, E.W.2    Kreisberg, R.3    Sun, Z.4
  • 31
    • 84902265781 scopus 로고    scopus 로고
    • MOPED 2.5-an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data
    • Montague, E., Stanberry, L., Higdon, R., Janko, I. et al., MOPED 2.5-an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. Omics J. Integr. Biol. 2014, 18, 335-343.
    • (2014) Omics J. Integr. Biol. , vol.18 , pp. 335-343
    • Montague, E.1    Stanberry, L.2    Higdon, R.3    Janko, I.4
  • 32
    • 84864817904 scopus 로고    scopus 로고
    • PaxDb, a database of protein abundance averages across all three domains of life
    • Wang, M., Weiss, M., Simonovic, M., Haertinger, G. et al., PaxDb, a database of protein abundance averages across all three domains of life. Mol. Cell. Proteomics 2012, 11, 492-500.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 492-500
    • Wang, M.1    Weiss, M.2    Simonovic, M.3    Haertinger, G.4
  • 33
    • 58149202157 scopus 로고    scopus 로고
    • Human Proteinpedia: a unified discovery resource for proteomics research
    • Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S. et al., Human Proteinpedia: a unified discovery resource for proteomics research. Nucl. Acids Res. 2009, 37, D773-D781.
    • (2009) Nucl. Acids Res. , vol.37 , pp. D773-D781
    • Kandasamy, K.1    Keerthikumar, S.2    Goel, R.3    Mathivanan, S.4
  • 34
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S. et al., A draft map of the human proteome. Nature 2014, 509, 575-581.
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1    Pinto, S.M.2    Getnet, D.3    Nirujogi, R.S.4
  • 35
    • 67650479361 scopus 로고    scopus 로고
    • NCBI peptidome: a new public repository for mass spectrometry peptide identifications
    • Slotta, D. J., Barrett, T., Edgar, R., NCBI peptidome: a new public repository for mass spectrometry peptide identifications. Nat. Biotechnol. 2009, 27, 600-601.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 600-601
    • Slotta, D.J.1    Barrett, T.2    Edgar, R.3
  • 37
    • 84891796097 scopus 로고    scopus 로고
    • ProteomeXchange provides globally coordinated proteomics data submission and dissemination
    • Vizcaino, J. A., Deutsch, E. W., Wang, R., Csordas, A. et al., ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32, 223-226.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 223-226
    • Vizcaino, J.A.1    Deutsch, E.W.2    Wang, R.3    Csordas, A.4
  • 38
    • 79952119025 scopus 로고    scopus 로고
    • Proteomics databases and repositories
    • Martens, L., Proteomics databases and repositories. Methods Mol. Biol. 2011, 694, 213-227.
    • (2011) Methods Mol. Biol. , vol.694 , pp. 213-227
    • Martens, L.1
  • 39
    • 77957220208 scopus 로고    scopus 로고
    • Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
    • Vizcaino, J. A., Foster, J. M., Martens, L., Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J. Proteomics 2010, 73, 2136-2146.
    • (2010) J. Proteomics , vol.73 , pp. 2136-2146
    • Vizcaino, J.A.1    Foster, J.M.2    Martens, L.3
  • 40
    • 61349182486 scopus 로고    scopus 로고
    • Recent developments in public proteomic MS repositories and pipelines
    • Mead, J. A., Bianco, L., Bessant, C., Recent developments in public proteomic MS repositories and pipelines. Proteomics 2009, 9, 861-881.
    • (2009) Proteomics , vol.9 , pp. 861-881
    • Mead, J.A.1    Bianco, L.2    Bessant, C.3
  • 41
    • 34548447191 scopus 로고    scopus 로고
    • Public proteomic MS repositories and pipelines: available tools and biological applications
    • Mead, J. A., Shadforth, I. P., Bessant, C., Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 2007, 7, 2769-2786.
    • (2007) Proteomics , vol.7 , pp. 2769-2786
    • Mead, J.A.1    Shadforth, I.P.2    Bessant, C.3
  • 42
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • The UniProtConsortium
    • The UniProtConsortium, Activities at the Universal Protein Resource (UniProt). Nucl. Acids Res. 2014, 42, D191-D198.
    • (2014) Nucl. Acids Res. , vol.42 , pp. D191-D198
  • 43
    • 84874083265 scopus 로고    scopus 로고
    • neXtProt: organizing protein knowledge in the context of Human Proteome Projects
    • Gaudet, P., Argoud-Puy, G., Cusin, I., Duek, P. et al., neXtProt: organizing protein knowledge in the context of Human Proteome Projects. J. Proteome Res. 2013, 12, 293-298.
    • (2013) J. Proteome Res. , vol.12 , pp. 293-298
    • Gaudet, P.1    Argoud-Puy, G.2    Cusin, I.3    Duek, P.4
  • 44
    • 79951924292 scopus 로고    scopus 로고
    • Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community
    • pe7
    • Olsen, J. V., Mann, M., Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community. Sci. Signal. 2011, 4, pe7.
    • (2011) Sci. Signal. , vol.4
    • Olsen, J.V.1    Mann, M.2
  • 46
    • 84859868686 scopus 로고    scopus 로고
    • The mzIdentML data standard for mass spectrometry-based proteomics results
    • M111014381
    • Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O. et al., The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012, 11, M111.014381.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Jones, A.R.1    Eisenacher, M.2    Mayer, G.3    Kohlbacher, O.4
  • 47
    • 84881104272 scopus 로고    scopus 로고
    • The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
    • Walzer, M., Qi, D., Mayer, G., Uszkoreit, J. et al., The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol. Cell. Proteomics 2013, 12, 2332-2340.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 2332-2340
    • Walzer, M.1    Qi, D.2    Mayer, G.3    Uszkoreit, J.4
  • 48
    • 8344284323 scopus 로고    scopus 로고
    • A common open representation of mass spectrometry data and its application to proteomics research
    • Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1459-1466
    • Pedrioli, P.G.1    Eng, J.K.2    Hubley, R.3    Vogelzang, M.4
  • 49
    • 77949676526 scopus 로고    scopus 로고
    • A guided tour of the trans-proteomic pipeline
    • Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T. et al., A guided tour of the trans-proteomic pipeline. Proteomics 2010, 10, 1150-1159.
    • (2010) Proteomics , vol.10 , pp. 1150-1159
    • Deutsch, E.W.1    Mendoza, L.2    Shteynberg, D.3    Farrah, T.4
  • 50
    • 84859843750 scopus 로고    scopus 로고
    • TraML-a standard format for exchange of selected reaction monitoring transition lists
    • R111015040
    • Deutsch, E. W., Chambers, M., Neumann, S., Levander, F. et al., TraML-a standard format for exchange of selected reaction monitoring transition lists. Mol. Cell. Proteomics 2012, 11, R111.015040.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Deutsch, E.W.1    Chambers, M.2    Neumann, S.3    Levander, F.4
  • 51
    • 84907951027 scopus 로고    scopus 로고
    • The mzTab data exchange format: communicating MS-based proteomics and metabolomics experimental results to a wider audience
    • mcpO113036681
    • Griss, J., Jones, A. R., Sachsenberg, T., Walzer, M. et al., The mzTab data exchange format: communicating MS-based proteomics and metabolomics experimental results to a wider audience. Mol. Cell. Proteomics 2014, pii, mcp.O113.036681.
    • (2014) Mol. Cell. Proteomics
    • Griss, J.1    Jones, A.R.2    Sachsenberg, T.3    Walzer, M.4
  • 52
    • 84890429234 scopus 로고    scopus 로고
    • Controlled vocabularies and ontologies in proteomics: overview, principles and practice
    • Mayer, G., Jones, A. R., Binz, P. A., Deutsch, E. W. et al., Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim. Biophys. Acta 2014, 1844, 98-107.
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 98-107
    • Mayer, G.1    Jones, A.R.2    Binz, P.A.3    Deutsch, E.W.4
  • 53
    • 77954255613 scopus 로고    scopus 로고
    • The ontology lookup service: bigger and better
    • Cote, R., Reisinger, F., Martens, L., Barsnes, H. et al., The ontology lookup service: bigger and better. Nucl. Acids Res. 2010, 38, W155-W160.
    • (2010) Nucl. Acids Res. , vol.38 , pp. W155-W160
    • Cote, R.1    Reisinger, F.2    Martens, L.3    Barsnes, H.4
  • 54
    • 84863011685 scopus 로고    scopus 로고
    • PRIDE inspector: a tool to visualize and validate MS proteomics data
    • Wang, R., Fabregat, A., Rios, D., Ovelleiro, D. et al., PRIDE inspector: a tool to visualize and validate MS proteomics data. Nat. Biotechnol. 2012, 30, 135-137.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 135-137
    • Wang, R.1    Fabregat, A.2    Rios, D.3    Ovelleiro, D.4
  • 55
    • 84870680444 scopus 로고    scopus 로고
    • The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
    • Cote, R. G., Griss, J., Dianes, J. A., Wang, R. et al., The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol. Cell. Proteomics 2012, 11, 1682-1689.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1682-1689
    • Cote, R.G.1    Griss, J.2    Dianes, J.A.3    Wang, R.4
  • 56
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 57
    • 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
  • 58
    • 84924611062 scopus 로고    scopus 로고
    • Standardization and guidelines: how to submit MS proteomics data to ProteomeXchange via the PRIDE database
    • in press.
    • Ternent, T., Csordas, A., Qi, D., Gomez-Baena, G. et al., Standardization and guidelines: how to submit MS proteomics data to ProteomeXchange via the PRIDE database. Proteomics 2014, in press.
    • (2014) Proteomics
    • Ternent, T.1    Csordas, A.2    Qi, D.3    Gomez-Baena, G.4
  • 60
    • 84873328157 scopus 로고    scopus 로고
    • PRIDE cluster: building a consensus of proteomics data
    • Griss, J., Foster, J. M., Hermjakob, H., Vizcaino, J. A., PRIDE cluster: building a consensus of proteomics data. Nat. Methods 2013, 10, 95-96.
    • (2013) Nat. Methods , vol.10 , pp. 95-96
    • Griss, J.1    Foster, J.M.2    Hermjakob, H.3    Vizcaino, J.A.4
  • 61
    • 79955595074 scopus 로고    scopus 로고
    • mProphet: automated data processing and statistical validation for large-scale SRM experiments
    • Reiter, L., Rinner, O., Picotti, P., Huttenhain, R. et al., mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 2011, 8, 430-435.
    • (2011) Nat. Methods , vol.8 , pp. 430-435
    • Reiter, L.1    Rinner, O.2    Picotti, P.3    Huttenhain, R.4
  • 62
    • 54049095667 scopus 로고    scopus 로고
    • A database of mass spectrometric assays for the yeast proteome
    • Picotti, P., Lam, H., Campbell, D., Deutsch, E. W. et al., A database of mass spectrometric assays for the yeast proteome. Nat. Methods 2008, 5, 913-914.
    • (2008) Nat. Methods , vol.5 , pp. 913-914
    • Picotti, P.1    Lam, H.2    Campbell, D.3    Deutsch, E.W.4
  • 63
    • 84874093356 scopus 로고    scopus 로고
    • The state of the human proteome in 2012 as viewed through PeptideAtlas
    • Farrah, T., Deutsch, E. W., Hoopmann, M. R., Hallows, J. L. et al., The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res. 2013, 12, 162-171.
    • (2013) J. Proteome Res. , vol.12 , pp. 162-171
    • Farrah, T.1    Deutsch, E.W.2    Hoopmann, M.R.3    Hallows, J.L.4
  • 64
    • 20144381803 scopus 로고    scopus 로고
    • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    • R9
    • Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P. et al., Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005, 6, R9.
    • (2005) Genome Biol. , vol.6
    • Desiere, F.1    Deutsch, E.W.2    Nesvizhskii, A.I.3    Mallick, P.4
  • 65
    • 79961176626 scopus 로고    scopus 로고
    • Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics
    • Lam, H., Aebersold, R., Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics. Methods 2011, 54, 424-431.
    • (2011) Methods , vol.54 , pp. 424-431
    • Lam, H.1    Aebersold, R.2
  • 66
    • 74049131716 scopus 로고    scopus 로고
    • High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    • Picotti, P., Rinner, O., Stallmach, R., Dautel, F. et al., High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Methods 2010, 7, 43-46.
    • (2010) Nat. Methods , vol.7 , pp. 43-46
    • Picotti, P.1    Rinner, O.2    Stallmach, R.3    Dautel, F.4
  • 67
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    • Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
    • (2008) EMBO Rep. , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 68
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25, 125-131.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 125-131
    • Mallick, P.1    Schirle, M.2    Chen, S.S.3    Flory, M.R.4
  • 69
    • 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
  • 70
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I., Keller, A., Kolker, E., Aebersold, R., A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
    • (2003) Anal. Chem. , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 71
    • 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. 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
  • 72
    • 79960124313 scopus 로고    scopus 로고
    • Using the Human Plasma PeptideAtlas to study human plasma proteins
    • Farrah, T., Deutsch, E. W., Aebersold, R., Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods Mol. Biol. 2011, 728, 349-374.
    • (2011) Methods Mol. Biol. , vol.728 , pp. 349-374
    • Farrah, T.1    Deutsch, E.W.2    Aebersold, R.3
  • 73
    • 29244477844 scopus 로고    scopus 로고
    • A human protein atlas for normal and cancer tissues based on antibody proteomics
    • Uhlen, M., Bjorling, E., Agaton, C., Szigyarto, C. A. et al., A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005, 4, 1920-1932.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1920-1932
    • Uhlen, M.1    Bjorling, E.2    Agaton, C.3    Szigyarto, C.A.4
  • 75
    • 84863229647 scopus 로고    scopus 로고
    • The chromosome-centric Human Proteome Project for cataloging proteins encoded in the genome
    • Paik, Y. K., Jeong, S. K., Omenn, G. S., Uhlen, M. et al., The chromosome-centric Human Proteome Project for cataloging proteins encoded in the genome. Nat. Biotechnol. 2012, 30, 221-223.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 221-223
    • Paik, Y.K.1    Jeong, S.K.2    Omenn, G.S.3    Uhlen, M.4
  • 76
    • 43049090085 scopus 로고    scopus 로고
    • Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
    • Lange, V., Malmstrom, J. A., Didion, J., King, N. L. et al., Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol. Cell. Proteomics 2008, 7, 1489-1500.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1489-1500
    • Lange, V.1    Malmstrom, J.A.2    Didion, J.3    King, N.L.4
  • 77
    • 79952703214 scopus 로고    scopus 로고
    • ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
    • Brusniak, M. Y., Kwok, S. T., Christiansen, M., Campbell, D. et al., ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinform. 2011, 12, 78.
    • (2011) BMC Bioinform. , vol.12 , pp. 78
    • Brusniak, M.Y.1    Kwok, S.T.2    Christiansen, M.3    Campbell, D.4
  • 78
    • 33646743767 scopus 로고    scopus 로고
    • The Gaggle: an open-source software system for integrating bioinformatics software and data sources
    • Shannon, P. T., Reiss, D. J., Bonneau, R., Baliga, N. S., The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinform. 2006, 7, 176.
    • (2006) BMC Bioinform. , vol.7 , pp. 176
    • Shannon, P.T.1    Reiss, D.J.2    Bonneau, R.3    Baliga, N.S.4
  • 79
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim, S., Gupta, N., Pevzner, P. A., Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 2008, 7, 3354-3363.
    • (2008) J. Proteome Res. , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 80
    • 58549101102 scopus 로고    scopus 로고
    • Discovery and revision of Arabidopsis genes by proteogenomics
    • Castellana, N. E., Payne, S. H., Shen, Z., Stanke, M. et al., Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl. Acad. Sci. USA 2008, 105, 21034-21038.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 21034-21038
    • Castellana, N.E.1    Payne, S.H.2    Shen, Z.3    Stanke, M.4
  • 81
    • 84891801883 scopus 로고    scopus 로고
    • Proteogenomic database construction driven from large scale RNA-seq data
    • Woo, S., Cha, S. W., Merrihew, G., He, Y. et al., Proteogenomic database construction driven from large scale RNA-seq data. J. Proteome Res. 2014, 13, 21-28.
    • (2014) J. Proteome Res. , vol.13 , pp. 21-28
    • Woo, S.1    Cha, S.W.2    Merrihew, G.3    He, Y.4
  • 82
    • 84891760451 scopus 로고    scopus 로고
    • An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays
    • Castellana, N. E., Shen, Z., He, Y., Walley, J. W. et al., An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol. Cell. Proteomics 2014, 13, 157-167.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 157-167
    • Castellana, N.E.1    Shen, Z.2    He, Y.3    Walley, J.W.4
  • 83
    • 84859877187 scopus 로고    scopus 로고
    • Fast multi-blind modification search through tandem mass spectrometry
    • M111010199
    • Na, S., Bandeira, N., Paek, E., Fast multi-blind modification search through tandem mass spectrometry. Mol. Cell. Proteomics 2012, 11, M111.010199.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Na, S.1    Bandeira, N.2    Paek, E.3
  • 85
    • 83055182134 scopus 로고    scopus 로고
    • Peptide identification by database search of mixture tandem mass spectra
    • M111010017
    • Wang, J., Bourne, P. E., Bandeira, N., Peptide identification by database search of mixture tandem mass spectra. Mol. Cell. Proteomics 2011, 10, M111.010017.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Wang, J.1    Bourne, P.E.2    Bandeira, N.3
  • 86
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: de novo peptide sequencing via probabilistic network modeling
    • Frank, A., Pevzner, P., PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
    • (2005) Anal. Chem. , vol.77 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 87
    • 84867161019 scopus 로고    scopus 로고
    • Shotgun protein sequencing with meta-contig assembly
    • Guthals, A., Clauser, K. R., Bandeira, N., Shotgun protein sequencing with meta-contig assembly. Mol. Cell. Proteomics 2012, 11, 1084-1096.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1084-1096
    • Guthals, A.1    Clauser, K.R.2    Bandeira, N.3
  • 89
    • 33747170146 scopus 로고    scopus 로고
    • Using annotated peptide mass spectrum libraries for protein identification
    • Craig, R., Cortens, J. C., Fenyo, D., Beavis, R. C., Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 2006, 5, 1843-1849.
    • (2006) J. Proteome Res. , vol.5 , pp. 1843-1849
    • Craig, R.1    Cortens, J.C.2    Fenyo, D.3    Beavis, R.C.4
  • 90
    • 21244443812 scopus 로고    scopus 로고
    • The use of proteotypic peptide libraries for protein identification
    • Craig, R., Cortens, J. P., Beavis, R. C., The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom. 2005, 19, 1844-1850.
    • (2005) Rapid Commun. Mass Spectrom. , vol.19 , pp. 1844-1850
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 91
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • The Gene Ontology Consortium.
    • Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4
  • 92
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M., Goto, S., KEGG: Kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 2000, 28, 27-30.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 93
    • 78651302604 scopus 로고    scopus 로고
    • The BRENDA tissue ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
    • Gremse, M., Chang, A., Schomburg, I., Grote, A. et al., The BRENDA tissue ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucl. Acids Res. 2011, 39, D507-D513.
    • (2011) Nucl. Acids Res. , vol.39 , pp. D507-D513
    • Gremse, M.1    Chang, A.2    Schomburg, I.3    Grote, A.4
  • 94
    • 84891818310 scopus 로고    scopus 로고
    • Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins
    • Lane, L., Bairoch, A., Beavis, R. C., Deutsch, E. W. et al., Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J. Proteome Res. 2014, 13, 15-20.
    • (2014) J. Proteome Res. , vol.13 , pp. 15-20
    • Lane, L.1    Bairoch, A.2    Beavis, R.C.3    Deutsch, E.W.4
  • 96
    • 79953701087 scopus 로고    scopus 로고
    • Andromeda: a peptide search engine integrated into the MaxQuant environment
    • Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
    • (2011) J. Proteome Res. , vol.10 , pp. 1794-1805
    • Cox, J.1    Neuhauser, N.2    Michalski, A.3    Scheltema, R.A.4
  • 97
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 98
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhausser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhausser, B.1    Busse, D.2    Li, N.3    Dittmar, G.4
  • 99
    • 84874750871 scopus 로고    scopus 로고
    • Corrigendum: global quantification of mammalian gene expression control
    • Schwanhausser, B., Busse, D., Li, N., Dittmar, G. et al., Corrigendum: global quantification of mammalian gene expression control. Nature 2013, 495, 126-127.
    • (2013) Nature , vol.495 , pp. 126-127
    • Schwanhausser, B.1    Busse, D.2    Li, N.3    Dittmar, G.4
  • 100
    • 84862209165 scopus 로고    scopus 로고
    • MOPED: model organism protein expression database
    • Kolker, E., Higdon, R., Haynes, W., Welch, D. et al., MOPED: model organism protein expression database. Nucl. Acids Res. 2012, 40, D1093-D1099.
    • (2012) Nucl. Acids Res. , vol.40 , pp. D1093-D1099
    • Kolker, E.1    Higdon, R.2    Haynes, W.3    Welch, D.4
  • 101
    • 84891772561 scopus 로고    scopus 로고
    • MOPED enables discoveries through consistently processed proteomics data
    • Higdon, R., Stewart, E., Stanberry, L., Haynes, W. et al., MOPED enables discoveries through consistently processed proteomics data. J. Proteome Res. 2014, 13, 107-113.
    • (2014) J. Proteome Res. , vol.13 , pp. 107-113
    • Higdon, R.1    Stewart, E.2    Stanberry, L.3    Haynes, W.4
  • 102
    • 84858743300 scopus 로고    scopus 로고
    • SPIRE: systematic protein investigative research environment
    • Kolker, E., Higdon, R., Morgan, P., Sedensky, M. et al., SPIRE: systematic protein investigative research environment. J. Proteomics 2011, 75, 122-126.
    • (2011) J. Proteomics , vol.75 , pp. 122-126
    • Kolker, E.1    Higdon, R.2    Morgan, P.3    Sedensky, M.4
  • 103
    • 78049480691 scopus 로고    scopus 로고
    • GeneCards Version 3: the human gene integrator
    • baq020
    • Safran, M., Dalah, I., Alexander, J., Rosen, N. et al., GeneCards Version 3: the human gene integrator. Database 2010, 2010, baq020.
    • (2010) Database , vol.2010
    • Safran, M.1    Dalah, I.2    Alexander, J.3    Rosen, N.4
  • 104
    • 79851505266 scopus 로고    scopus 로고
    • Reactome knowledgebase of human biological pathways and processes
    • D'Eustachio, P., Reactome knowledgebase of human biological pathways and processes. Methods Mol. Biol. 2011, 694, 49-61.
    • (2011) Methods Mol. Biol. , vol.694 , pp. 49-61
    • D'Eustachio, P.1
  • 105
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M. et al., The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucl. Acids Res. 2011, 39, D561-D568.
    • (2011) Nucl. Acids Res. , vol.39 , pp. D561-D568
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4
  • 106
    • 77949686097 scopus 로고    scopus 로고
    • Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome
    • Weiss, M., Schrimpf, S., Hengartner, M. O., Lercher, M. J., von Mering, C., Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Proteomics 2010, 10, 1297-1306.
    • (2010) Proteomics , vol.10 , pp. 1297-1306
    • Weiss, M.1    Schrimpf, S.2    Hengartner, M.O.3    Lercher, M.J.4    von Mering, C.5
  • 108
    • 84855658379 scopus 로고    scopus 로고
    • Human protein reference database and Human Proteinpedia as resources for phosphoproteome analysis
    • Goel, R., Harsha, H. C., Pandey, A., Prasad, T. S., Human protein reference database and Human Proteinpedia as resources for phosphoproteome analysis. Mol. BioSyst. 2012, 8, 453-463.
    • (2012) Mol. BioSyst. , vol.8 , pp. 453-463
    • Goel, R.1    Harsha, H.C.2    Pandey, A.3    Prasad, T.S.4
  • 110
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J. K., McCormack, A. L., Yates, J. R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 111
    • 84886089276 scopus 로고    scopus 로고
    • Integration of cardiac proteome biology and medicine by a specialized knowledgebase
    • Zong, N. C., Li, H., Li, H., Lam, M. P. et al., Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circ. Res. 2013, 113, 1043-1053.
    • (2013) Circ. Res. , vol.113 , pp. 1043-1053
    • Zong, N.C.1    Li, H.2    Li, H.3    Lam, M.P.4
  • 112
    • 79952531916 scopus 로고    scopus 로고
    • pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana
    • Baerenfaller, K., Hirsch-Hoffmann, M., Svozil, J., Hull, R. et al., pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana. Integr. Biol. 2011, 3, 225-237.
    • (2011) Integr. Biol. , vol.3 , pp. 225-237
    • Baerenfaller, K.1    Hirsch-Hoffmann, M.2    Svozil, J.3    Hull, R.4
  • 113
    • 84866054140 scopus 로고    scopus 로고
    • pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool
    • Hirsch-Hoffmann, M., Gruissem, W., Baerenfaller, K., pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool. Front. Plant Sci. 2012, 3, 123.
    • (2012) Front. Plant Sci. , vol.3 , pp. 123
    • Hirsch-Hoffmann, M.1    Gruissem, W.2    Baerenfaller, K.3
  • 114
    • 36448936713 scopus 로고    scopus 로고
    • PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra
    • Roos, F. F., Jacob, R., Grossmann, J., Fischer, B. et al., PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics 2007, 23, 3016-3023.
    • (2007) Bioinformatics , vol.23 , pp. 3016-3023
    • Roos, F.F.1    Jacob, R.2    Grossmann, J.3    Fischer, B.4
  • 115
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • UniProt, C., Activities at the Universal Protein Resource (UniProt). Nucl. Acids Res. 2014, 42, D191-D198.
    • (2014) Nucl. Acids Res. , vol.42 , pp. D191-D198
    • UniProt, C.1
  • 116
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B. et al., PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucl. Acids Res. 2012, 40, D261-D270.
    • (2012) Nucl. Acids Res. , vol.40 , pp. D261-D270
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4
  • 117
    • 84890644637 scopus 로고    scopus 로고
    • Status of large-scale analysis of post-translational modifications by mass spectrometry
    • Olsen, J. V., Mann, M., Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol. Cell. Proteomics 2013, 12, 3444-3452.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3444-3452
    • Olsen, J.V.1    Mann, M.2
  • 118
    • 34247375985 scopus 로고    scopus 로고
    • Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry
    • Asara, J. M., Schweitzer, M. H., Freimark, L. M., Phillips, M., Cantley, L. C., Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 2007, 316, 280-285.
    • (2007) Science , vol.316 , pp. 280-285
    • Asara, J.M.1    Schweitzer, M.H.2    Freimark, L.M.3    Phillips, M.4    Cantley, L.C.5
  • 119
  • 120
    • 70349925705 scopus 로고    scopus 로고
    • Reanalysis of Tyrannosaurus rex mass spectra
    • Bern, M., Phinney, B. S., Goldberg, D., Reanalysis of Tyrannosaurus rex mass spectra. J. Proteome Res. 2009, 8, 4328-4332.
    • (2009) J. Proteome Res. , vol.8 , pp. 4328-4332
    • Bern, M.1    Phinney, B.S.2    Goldberg, D.3
  • 121
    • 78049248014 scopus 로고    scopus 로고
    • Iridovirus and microsporidian linked to honey bee colony decline
    • Bromenshenk, J. J., Henderson, C. B., Wick, C. H., Stanford, M. F. et al., Iridovirus and microsporidian linked to honey bee colony decline. PloSOne 2010, 5, e13181.
    • (2010) PloSOne , vol.5 , pp. e13181
    • Bromenshenk, J.J.1    Henderson, C.B.2    Wick, C.H.3    Stanford, M.F.4
  • 122
    • 84860334002 scopus 로고    scopus 로고
    • Bromenshenk (PLoS One, 2011, 5(10):e13181) have claimed to have found peptides from an invertebrate iridovirus in bees
    • A1100063871
    • Foster, L. J., Bromenshenk et al. (PLoS One, 2011, 5(10):e13181) have claimed to have found peptides from an invertebrate iridovirus in bees. Mol. Cell. Proteomics 2012, 11, A110.0063871.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Foster, L.J.1
  • 123
    • 84867186895 scopus 로고    scopus 로고
    • Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data
    • Hahne, H., Kuster, B., Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data. Mol. Cell. Proteomics 2012, 11, 1063-1069.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1063-1069
    • Hahne, H.1    Kuster, B.2
  • 124
    • 84864474310 scopus 로고    scopus 로고
    • Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites
    • Matic, I., Ahel, I., Hay, R. T., Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat. Methods 2012, 9, 771-772.
    • (2012) Nat. Methods , vol.9 , pp. 771-772
    • Matic, I.1    Ahel, I.2    Hay, R.T.3
  • 125
    • 79955555530 scopus 로고    scopus 로고
    • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
    • Brosch, M., Saunders, G. I., Frankish, A., Collins, M. O. et al., Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res. 2011, 21, 756-767.
    • (2011) Genome Res. , vol.21 , pp. 756-767
    • Brosch, M.1    Saunders, G.I.2    Frankish, A.3    Collins, M.O.4
  • 126
    • 84899997891 scopus 로고    scopus 로고
    • PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments
    • Mohammed, Y., Domanski, D., Jackson, A. M., Smith, D. S. et al., PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J. Proteomics 2014, 106C, 151-161.
    • (2014) J. Proteomics , vol.106 C , pp. 151-161
    • Mohammed, Y.1    Domanski, D.2    Jackson, A.M.3    Smith, D.S.4
  • 127
    • 84866303718 scopus 로고    scopus 로고
    • MRMaid 2.0: mining PRIDE for evidence-based SRM transitions
    • Fan, J., Mohareb, F., Bond, N. J., Lilley, K. S., Bessant, C., MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS 2012, 16, 483-488.
    • (2012) OMICS , vol.16 , pp. 483-488
    • Fan, J.1    Mohareb, F.2    Bond, N.J.3    Lilley, K.S.4    Bessant, C.5
  • 128
    • 80052720895 scopus 로고    scopus 로고
    • Published and perished? The influence of the searched protein database on the long-term storage of proteomics data
    • M111008490
    • Griss, J., Cote, R. G., Gerner, C., Hermjakob, H., Vizcaino, J. A., Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. Mol. Cell. Proteomics 2011, 10, M111.008490.
    • (2011) Mol. Cell. Proteomics , vol.10
    • Griss, J.1    Cote, R.G.2    Gerner, C.3    Hermjakob, H.4    Vizcaino, J.A.5
  • 129
    • 38649129380 scopus 로고    scopus 로고
    • Analyzing large-scale proteomics projects with latent semantic indexing
    • Klie, S., Martens, L., Vizcaino, J. A., Cote, R. et al., Analyzing large-scale proteomics projects with latent semantic indexing. J. Proteome Res. 2008, 7, 182-191.
    • (2008) J. Proteome Res. , vol.7 , pp. 182-191
    • Klie, S.1    Martens, L.2    Vizcaino, J.A.3    Cote, R.4
  • 130
    • 41549097236 scopus 로고    scopus 로고
    • Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
    • Mueller, M., Vizcaino, J. A., Jones, P., Cote, R. et al., Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 2008, 8, 1138-1148.
    • (2008) Proteomics , vol.8 , pp. 1138-1148
    • Mueller, M.1    Vizcaino, J.A.2    Jones, P.3    Cote, R.4
  • 132
    • 79956281509 scopus 로고    scopus 로고
    • A posteriori quality control for the curation and reuse of public proteomics data
    • Foster, J. M., Degroeve, S., Gatto, L., Visser, M. et al., A posteriori quality control for the curation and reuse of public proteomics data. Proteomics 2011, 11, 2182-2194.
    • (2011) Proteomics , vol.11 , pp. 2182-2194
    • Foster, J.M.1    Degroeve, S.2    Gatto, L.3    Visser, M.4
  • 133
    • 80055109819 scopus 로고    scopus 로고
    • Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets
    • Griss, J., Martin, M., O'Donovan, C., Apweiler, R. et al., Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics 2011, 11, 4434-4438.
    • (2011) Proteomics , vol.11 , pp. 4434-4438
    • Griss, J.1    Martin, M.2    O'Donovan, C.3    Apweiler, R.4
  • 134
    • 79952356891 scopus 로고    scopus 로고
    • Compomics utilities: an open-source Java library for computational proteomics
    • Barsnes, H., Vaudel, M., Colaert, N., Helsens, K. et al., Compomics utilities: an open-source Java library for computational proteomics. BMC Bioinformatics 2011, 12, 70.
    • (2011) BMC Bioinformatics , vol.12 , pp. 70
    • Barsnes, H.1    Vaudel, M.2    Colaert, N.3    Helsens, K.4
  • 135
    • 79951750784 scopus 로고    scopus 로고
    • SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
    • Vaudel, M., Barsnes, H., Berven, F. S., Sickmann, A., Martens, L., SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011, 11, 996-999.
    • (2011) Proteomics , vol.11 , pp. 996-999
    • Vaudel, M.1    Barsnes, H.2    Berven, F.S.3    Sickmann, A.4    Martens, L.5
  • 137
    • 84901949876 scopus 로고    scopus 로고
    • SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data
    • Zhu, Y., Hultin-Rosenberg, L., Forshed, J., Branca, R. M. et al., SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data. Mol. Cell. Proteomics 2014, 13, 1552-1562.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1552-1562
    • Zhu, Y.1    Hultin-Rosenberg, L.2    Forshed, J.3    Branca, R.M.4
  • 138
    • 84878631292 scopus 로고    scopus 로고
    • Resilience in the proteomics data ecosystem: how the field cares for its data
    • Martens, L., Resilience in the proteomics data ecosystem: how the field cares for its data. Proteomics 2013, 13, 1548-1550.
    • (2013) Proteomics , vol.13 , pp. 1548-1550
    • Martens, L.1
  • 139
    • 84879501266 scopus 로고    scopus 로고
    • Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report
    • Perez-Riverol, Y., Hermjakob, H., Kohlbacher, O., Martens, L. et al., Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J. Proteomics 2013, 87, 134-138.
    • (2013) J. Proteomics , vol.87 , pp. 134-138
    • Perez-Riverol, Y.1    Hermjakob, H.2    Kohlbacher, O.3    Martens, L.4
  • 140
    • 84878652909 scopus 로고    scopus 로고
    • From Peptidome to PRIDE: public proteomics data migration at a large scale
    • Csordas, A., Wang, R., Rios, D., Reisinger, F. et al., From Peptidome to PRIDE: public proteomics data migration at a large scale. Proteomics 2013, 13, 1692-1695.
    • (2013) Proteomics , vol.13 , pp. 1692-1695
    • Csordas, A.1    Wang, R.2    Rios, D.3    Reisinger, F.4
  • 141
    • 84862186859 scopus 로고    scopus 로고
    • The BioSample database (BioSD) at the European Bioinformatics Institute
    • Gostev, M., Faulconbridge, A., Brandizi, M., Fernandez-Banet, J. et al., The BioSample database (BioSD) at the European Bioinformatics Institute. Nucl. Acids Res. 2012, 40, D64-D70.
    • (2012) Nucl. Acids Res. , vol.40 , pp. D64-D70
    • Gostev, M.1    Faulconbridge, A.2    Brandizi, M.3    Fernandez-Banet, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.