-
1
-
-
0036535357
-
Analysis of quantitative proteomic data generated via multidimensional protein identification technology
-
Washburn, M. P., Ulaszek, R., Deciu, C., Schieltz, D. M., Yates, J. R., III, Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 2002, 74, 1650-1657.
-
(2002)
Anal. Chem.
, vol.74
, pp. 1650-1657
-
-
Washburn, M.P.1
Ulaszek, R.2
Deciu, C.3
Schieltz, D.M.4
Yates III, J.R.5
-
2
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J. K., McCormack, L., Yates, A., Yates, J. R., III, 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, L.2
Yates, A.3
Yates III, J.R.4
-
3
-
-
35648943746
-
ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program
-
Xu, T., Venable, J. D., Park, S. K., Cociorva, D. et al., ProLuCID, a fast and sensitive tandem mass spectra-based protein identification program. Mol. Cell. Proteomics 2006, 5, S174.
-
(2006)
Mol. Cell. Proteomics
, vol.5
-
-
Xu, T.1
Venable, J.D.2
Park, S.K.3
Cociorva, D.4
-
4
-
-
33847401893
-
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
-
Tabb, D. L., Fernando, C. G., Chambers, M. C., MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 2007, 6, 654-661.
-
(2007)
J. Proteome Res.
, vol.6
, pp. 654-661
-
-
Tabb, D.L.1
Fernando, C.G.2
Chambers, M.C.3
-
5
-
-
67449100431
-
Validation of tandem mass spectrometry database search results using DTASelect
-
Chapter 13
-
Cociorva, D., Tabb, L., Yates, J. R., Validation of tandem mass spectrometry database search results using DTASelect. Curr. Protoc. Bioinformatics 2006, Chapter 13, 13.4.1-13.4.14.
-
(2006)
Curr. Protoc. Bioinformatics
, pp. 1341-13414
-
-
Cociorva, D.1
Tabb, L.2
Yates, J.R.3
-
6
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
Kall, L., Canterbury, J. D., Weston, J., Noble, W. S., MacCoss, M. J., Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 2007, 4, 923-925.
-
(2007)
Nat. Methods
, vol.4
, pp. 923-925
-
-
Kall, L.1
Canterbury, J.D.2
Weston, J.3
Noble, W.S.4
MacCoss, M.J.5
-
7
-
-
68549092907
-
IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering
-
Ma, Z. Q., Dasari, S., Chambers, M. C., Litton, M. D. et al., IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering. J. Proteome Res. 2009, 8, 3872-3881.
-
(2009)
J. Proteome Res.
, vol.8
, pp. 3872-3881
-
-
Ma, Z.Q.1
Dasari, S.2
Chambers, M.C.3
Litton, M.D.4
-
8
-
-
41349096900
-
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
-
Deutsch, E. W., Lam, H., Aebersold, R., Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol. Genomics 2008, 33, 18-25.
-
(2008)
Physiol. Genomics
, vol.33
, pp. 18-25
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
9
-
-
0037108887
-
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
-
10
-
-
0037277179
-
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome
-
Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., Gygi, S. P., Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2003, 2, 43-50.
-
(2003)
J. Proteome Res.
, vol.2
, pp. 43-50
-
-
Peng, J.1
Elias, J.E.2
Thoreen, C.C.3
Licklider, L.J.4
Gygi, S.P.5
-
11
-
-
48249119082
-
PatternLab for proteomics: a tool for differential shotgun proteomics
-
Carvalho, P. C., Fischer, J. S., Chen, E. I., Yates, J. R., III, Barbosa, V. C., PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics 2008, 9, 316.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 316
-
-
Carvalho, P.C.1
Fischer, J.S.2
Chen, E.I.3
Yates III, J.R.4
Barbosa, V.C.5
-
12
-
-
70350018231
-
YADA: a tool for taking the most out of high-resolution spectra
-
Carvalho, P. C., Xu, T., Han, X., Cociorva, D. et al., YADA: a tool for taking the most out of high-resolution spectra. Bioinformatics 2009, 25, 2735-2736.
-
(2009)
Bioinformatics
, vol.25
, pp. 2735-2736
-
-
Carvalho, P.C.1
Xu, T.2
Han, X.3
Cociorva, D.4
-
13
-
-
62549085665
-
GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data
-
Carvalho, P. C., Fischer, J. S., Chen, E. I., Domont, G. B. et al., GO Explorer: a gene-ontology tool to aid in the interpretation of shotgun proteomics data. Proteome Sci. 2009, 7, 6.
-
(2009)
Proteome Sci.
, vol.7
, pp. 6
-
-
Carvalho, P.C.1
Fischer, J.S.2
Chen, E.I.3
Domont, G.B.4
-
14
-
-
78651418570
-
Analyzing marginal cases in differential shotgun proteomics
-
Carvalho, P. C., Fischer, J. S., Perales, J., Yates, J. R. et al., Analyzing marginal cases in differential shotgun proteomics. Bioinformatics 2011, 27, 275-276.
-
(2011)
Bioinformatics
, vol.27
, pp. 275-276
-
-
Carvalho, P.C.1
Fischer, J.S.2
Perales, J.3
Yates, J.R.4
-
15
-
-
77953865293
-
Analyzing shotgun proteomic data with PatternLab for proteomics
-
Chapter 13
-
Carvalho, P. C., Yates, I., Jr., Barbosa, V. C., Analyzing shotgun proteomic data with PatternLab for proteomics. Curr. Protoc. Bioinformatics 2010, Chapter 13, 13.13.1-13.13.15.
-
(2010)
Curr. Protoc. Bioinformatics
, pp. 13131-131315
-
-
Carvalho, P.C.1
Yates Jr., I.2
Barbosa, V.C.3
-
16
-
-
0034069495
-
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
-
17
-
-
80054024254
-
Can the false-discovery rate be misleading
-
Barboza, R., Cociorva, D., Xu, T., Barbosa, V. C. et al., Can the false-discovery rate be misleading? Proteomics 2011, 11, 4105-4108.
-
(2011)
Proteomics
, vol.11
, pp. 4105-4108
-
-
Barboza, R.1
Cociorva, D.2
Xu, T.3
Barbosa, V.C.4
-
18
-
-
82255181179
-
Arginylation and methylation double up to regulate nuclear proteins and nuclear architecture in vivo
-
Saha, S., Wong, C. C., Xu, T., Namgoong, S. et al., Arginylation and methylation double up to regulate nuclear proteins and nuclear architecture in vivo. Chem. Biol. 2011, 18, 1369-1378.
-
(2011)
Chem. Biol.
, vol.18
, pp. 1369-1378
-
-
Saha, S.1
Wong, C.C.2
Xu, T.3
Namgoong, S.4
-
19
-
-
0042338362
-
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
|