-
1
-
-
38649083118
-
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
-
Kall, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res. 7, 29-34
-
(2008)
J Proteome Res.
, vol.7
, pp. 29-34
-
-
Kall, L.1
Storey, J.D.2
Maccoss, M.J.3
Noble, W.S.4
-
2
-
-
84873387053
-
When target-decoy false discovery rate estimations are inaccurate and how to spot instances
-
Chalkley, R. J. (2013) When target-decoy false discovery rate estimations are inaccurate and how to spot instances. J. Proteome Res. 12, 1062-1064
-
(2013)
J. Proteome Res.
, vol.12
, pp. 1062-1064
-
-
Chalkley, R.J.1
-
3
-
-
84860879590
-
Modification site localization scoring: Strategies and performance
-
Chalkley, R. J., and Clauser, K. R. (2012) Modification site localization scoring: Strategies and performance. Mol. Cell. Proteomics 11, 3-14
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 3-14
-
-
Chalkley, R.J.1
Clauser, K.R.2
-
4
-
-
33646907086
-
Reporting protein identification data: The next generation of guidelines
-
Bradshaw, R. A., Burlingame, A. L., Carr, S., and Aebersold, R. (2006) Reporting protein identification data: The next generation of guidelines. Mol. Cell. Proteomics 5, 787-788
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 787-788
-
-
Bradshaw, R.A.1
Burlingame, A.L.2
Carr, S.3
Aebersold, R.4
-
5
-
-
84870721324
-
File formats commonly used in mass spectrometry proteomics
-
Deutsch, E. W. (2012) File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 11, 1612-1621
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1612-1621
-
-
Deutsch, E.W.1
-
6
-
-
77949695293
-
Scaffold: A bioinformatic tool for validating MS/MSbased proteomic studies
-
Searle, B. C. (2010) Scaffold: A bioinformatic tool for validating MS/MSbased proteomic studies. Proteomics 10, 1265-1269
-
(2010)
Proteomics
, vol.10
, pp. 1265-1269
-
-
Searle, B.C.1
-
7
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
-
(2004)
J. Proteome Res.
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
Xu, M.5
Maynard, D.M.6
Yang, X.7
Shi, W.8
Bryant, S.H.9
-
8
-
-
79955778900
-
MzResults: An interactive viewer for interrogation and distribution of proteomics results
-
Webber, J. T., Askenazi, M., and Marto, J. A. (2011) mzResults: An interactive viewer for interrogation and distribution of proteomics results. Mol. Cell. Proteomics 10, M110.003970
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. 110003970
-
-
Webber, J.T.1
Askenazi, M.2
Marto, J.A.3
-
9
-
-
84859868686
-
The mzIdentML data standard for mass spectrometry-based proteomics results
-
Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., Selley, J. N., Searle, B. C., Shofstahl, J., Seymour, S. L., Julian, R., Binz, P. A., Deutsch, E. W., Hermjakob, H., Reisinger, F., Griss, J., Vizcaino, J. A., Chambers, M., Pizarro, A., and Creasy, D. (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 11, M111.014381
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 111014381
-
-
Jones, A.R.1
Eisenacher, M.2
Mayer, G.3
Kohlbacher, O.4
Siepen, J.5
Hubbard, S.J.6
Selley, J.N.7
Searle, B.C.8
Shofstahl, J.9
Seymour, S.L.10
Julian, R.11
Binz, P.A.12
Deutsch, E.W.13
Hermjakob, H.14
Reisinger, F.15
Griss, J.16
Vizcaino, J.A.17
Chambers, M.18
Pizarro, A.19
Creasy, D.20
more..
-
10
-
-
70349091863
-
A guide to the Proteomics Identifications Database proteomics data repository
-
Vizcaino, J. A., Cote, R., Reisinger, F., Foster, J. M., Mueller, M., Rameseder, J., Hermjakob, H., and Martens, L. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9, 4276-4283
-
(2009)
Proteomics
, vol.9
, pp. 4276-4283
-
-
Vizcaino, J.A.1
Cote, R.2
Reisinger, F.3
Foster, J.M.4
Mueller, M.5
Rameseder, J.6
Hermjakob, H.7
Martens, L.8
-
11
-
-
49449097859
-
The PSI-MOD community standard for representation of protein modification data
-
Montecchi-Palazzi, L., Beavis, R., Binz, P. A., Chalkley, R. J., Cottrell, J., Creasy, D., Shofstahl, J., Seymour, S. L., and Garavelli, J. S. (2008) The PSI-MOD community standard for representation of protein modification data. Nat. Biotechnol. 26, 864-866
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 864-866
-
-
Montecchi-Palazzi, L.1
Beavis, R.2
Binz, P.A.3
Chalkley, R.J.4
Cottrell, J.5
Creasy, D.6
Shofstahl, J.7
Seymour, S.L.8
Garavelli, J.S.9
-
13
-
-
84893336659
-
Matching cross-linked peptide spectra: Only as good as the worse identification
-
Trnka, M. J., Baker, P. R., Robinson, P. J., Burlingame, A. L., and Chalkley, R. J. (2014) Matching cross-linked peptide spectra: Only as good as the worse identification. Mol. Cell. Proteomics 13, 420-434
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 420-434
-
-
Trnka, M.J.1
Baker, P.R.2
Robinson, P.J.3
Burlingame, A.L.4
Chalkley, R.J.5
-
14
-
-
84874616810
-
The DegraBase: A database of proteolysis in healthy and apoptotic human cells
-
Crawford, E. D., Seaman, J. E., Agard, N., Hsu, G. W., Julien, O., Mahrus, S., Nguyen, H., Shimbo, K., Yoshihara, H. A., Zhuang, M., Chalkley, R. J., and Wells, J. A. (2013) The DegraBase: A database of proteolysis in healthy and apoptotic human cells. Mol. Cell. Proteomics 12, 813-824
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 813-824
-
-
Crawford, E.D.1
Seaman, J.E.2
Agard, N.3
Hsu, G.W.4
Julien, O.5
Mahrus, S.6
Nguyen, H.7
Shimbo, K.8
Yoshihara, H.A.9
Zhuang, M.10
Chalkley, R.J.11
Wells, J.A.12
-
15
-
-
79960181605
-
Modification site localization scoring integrated into a search engine
-
Baker, P. R., Trinidad, J. C., and Chalkley, R. J. (2011) Modification site localization scoring integrated into a search engine. Mol. Cell. Proteomics 10, M111.008078
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. 111008078
-
-
Baker, P.R.1
Trinidad, J.C.2
Chalkley, R.J.3
-
16
-
-
84863011685
-
PRIDE Inspector: A tool to visualize and validate MS proteomics data
-
Wang, R., Fabregat, A., Rios, D., Ovelleiro, D., Foster, J. M., Cote, R. G., Griss, J., Csordas, A., Perez-Riverol, Y., Reisinger, F., Hermjakob, H., Martens, L., and Vizcaino, J. A. (2012) PRIDE Inspector: A tool to visualize and validate MS proteomics data. Nat. Biotechnol. 30, 135-137
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 135-137
-
-
Wang, R.1
Fabregat, A.2
Rios, D.3
Ovelleiro, D.4
Foster, J.M.5
Cote, R.G.6
Griss, J.7
Csordas, A.8
Perez-Riverol, Y.9
Reisinger, F.10
Hermjakob, H.11
Martens, L.12
Vizcaino, J.A.13
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