-
1
-
-
0037435030
-
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
-
-
84855269263
-
Computational mass spectrometry-based proteomics
-
Käll L., Vitek O. Computational mass spectrometry-based proteomics. PLoS Comput Biol 2011, 7:e1002277.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Käll, L.1
Vitek, O.2
-
3
-
-
84857476737
-
Computational and statistical analysis of protein mass spectrometry data
-
Noble W., MacCoss M. Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol 2012, 8:e1002296.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Noble, W.1
MacCoss, M.2
-
4
-
-
79952309062
-
Quality assessments of peptide-spectrum matches in shotgun proteomics
-
Granholm V., Käll L. Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 2011, 11:1086-1093.
-
(2011)
Proteomics
, vol.11
, pp. 1086-1093
-
-
Granholm, V.1
Käll, L.2
-
5
-
-
0000453490
-
Statistical "discoveries" and effect-size estimation
-
Sorić B. Statistical "discoveries" and effect-size estimation. J Am Stat Assoc 1989, 84:608-610.
-
(1989)
J Am Stat Assoc
, vol.84
, pp. 608-610
-
-
Sorić, B.1
-
6
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 1995, 57:289-300.
-
(1995)
J R Stat Soc Ser B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
7
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey J., Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100:9440.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 9440
-
-
Storey, J.1
Tibshirani, R.2
-
8
-
-
0036209134
-
Qscore: an algorithm for evaluating SEQUEST database search results
-
Moore R., Young M., Lee T. Qscore: an algorithm for evaluating SEQUEST database search results. J Am Soc Mass Spectrom 2002, 13:378-386.
-
(2002)
J Am Soc Mass Spectrom
, vol.13
, pp. 378-386
-
-
Moore, R.1
Young, M.2
Lee, T.3
-
9
-
-
77449146854
-
Target-decoy search strategy for mass spectrometry-based proteomics
-
Elias J., Gygi S. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol 2010, 604:55.
-
(2010)
Methods Mol Biol
, vol.604
, pp. 55
-
-
Elias, J.1
Gygi, S.2
-
10
-
-
0037442649
-
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
-
Fenyö D., Beavis R. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 2003, 75:768-774.
-
(2003)
Anal Chem
, vol.75
, pp. 768-774
-
-
Fenyö, D.1
Beavis, R.2
-
11
-
-
65249097774
-
Statistical calibration of the SEQUEST XCorr function
-
Klammer A., Park C., Noble W. Statistical calibration of the SEQUEST XCorr function. J Proteome Res 2009, 8:2106-2113.
-
(2009)
J Proteome Res
, vol.8
, pp. 2106-2113
-
-
Klammer, A.1
Park, C.2
Noble, W.3
-
12
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller A., Nesvizhskii A., 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.2
Kolker, E.3
Aebersold, R.4
-
13
-
-
50149117169
-
Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
-
Kim S., Gupta N., Pevzner P. 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.3
-
14
-
-
0035047188
-
Peptidomics the comprehensive analysis of peptides in complex biological mixtures
-
Schulz-Knappe P., Hans-Dieter Z., Heine G., Jurgens M., Schrader M. Peptidomics the comprehensive analysis of peptides in complex biological mixtures. Comb Chem High Throughput Screen 2001, 4:207-217.
-
(2001)
Comb Chem High Throughput Screen
, vol.4
, pp. 207-217
-
-
Schulz-Knappe, P.1
Hans-Dieter, Z.2
Heine, G.3
Jurgens, M.4
Schrader, M.5
-
15
-
-
0042338362
-
A statistical model for identifying proteins by tandem mass spectrometry
-
Nesvizhskii A., 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.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
16
-
-
57449099865
-
Maxquant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification
-
Cox J., Mann M. Maxquant enables high peptide identification rates, individualized ppb-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
-
17
-
-
77957339566
-
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data
-
Serang O., MacCoss M., Noble W. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J Proteome Res 2010, 9:5346-5357.
-
(2010)
J Proteome Res
, vol.9
, pp. 5346-5357
-
-
Serang, O.1
MacCoss, M.2
Noble, W.3
-
18
-
-
72149093828
-
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
-
Reiter L., Claassen M., Schrimpf S., Jovanovic M., Schmidt A., Buhmann J., et al. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics 2009, 8:2405.
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 2405
-
-
Reiter, L.1
Claassen, M.2
Schrimpf, S.3
Jovanovic, M.4
Schmidt, A.5
Buhmann, J.6
-
19
-
-
82755181926
-
Two-dimensional target decoy strategy for shotgun proteomics
-
Bern M., Kil Y. Two-dimensional target decoy strategy for shotgun proteomics. J Proteome Res 2011, 10:5296-5301.
-
(2011)
J Proteome Res
, vol.10
, pp. 5296-5301
-
-
Bern, M.1
Kil, Y.2
-
20
-
-
21044459357
-
A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results
-
Weatherly D., Atwood J., Minning T., Cavola C., Tarleton R., Orlando R. A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results. Mol Cell Proteomics 2005, 4:762.
-
(2005)
Mol Cell Proteomics
, vol.4
, pp. 762
-
-
Weatherly, D.1
Atwood, J.2
Minning, T.3
Cavola, C.4
Tarleton, R.5
Orlando, R.6
-
21
-
-
35748972060
-
Semi-supervised learning for peptide identification from shotgun proteomics datasets
-
Käll L., Canterbury J., Weston J., Noble W., MacCoss M. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 4:923-925.
-
(2007)
Nat Methods
, vol.4
, pp. 923-925
-
-
Käll, L.1
Canterbury, J.2
Weston, J.3
Noble, W.4
MacCoss, M.5
-
22
-
-
51349096085
-
Improved ranking functions for protein and modification-site identifications
-
Bern M., Goldberg D. Improved ranking functions for protein and modification-site identifications. J Comput Biol 2008, 15:705-719.
-
(2008)
J Comput Biol
, vol.15
, pp. 705-719
-
-
Bern, M.1
Goldberg, D.2
-
23
-
-
80053387432
-
IProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
-
Shteynberg D., Deutsch E., Lam H., Eng J., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011, 10.
-
(2011)
Mol Cell Proteomics
, vol.10
-
-
Shteynberg, D.1
Deutsch, E.2
Lam, H.3
Eng, J.4
Sun, Z.5
Tasman, N.6
-
24
-
-
77957221582
-
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
-
Nesvizhskii A. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010, 73:2092-2123.
-
(2010)
J Proteomics
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.1
-
25
-
-
79955870431
-
On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics
-
Granholm V., Noble W., Käll L. On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics. J Proteome Res 2011, 10:2671-2678.
-
(2011)
J Proteome Res
, vol.10
, pp. 2671-2678
-
-
Granholm, V.1
Noble, W.2
Käll, L.3
-
26
-
-
38649083118
-
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
-
Käll L., Storey J., MacCoss M., Noble W. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 2008, 7:29-34.
-
(2008)
J Proteome Res
, vol.7
, pp. 29-34
-
-
Käll, L.1
Storey, J.2
MacCoss, M.3
Noble, W.4
-
28
-
-
1542784653
-
Empirical Bayes analysis of a microarray experiment
-
Efron B., Tibshirani R., Storey J., Tusher V. Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc 2001, 96:1151-1160.
-
(2001)
J Am Stat Assoc
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.3
Tusher, V.4
-
29
-
-
0036020892
-
A direct approach to false discovery rates
-
Storey J. A direct approach to false discovery rates. J R Stat Soc Ser B (Stat Methodol) 2002, 64:479-498.
-
(2002)
J R Stat Soc Ser B (Stat Methodol)
, vol.64
, pp. 479-498
-
-
Storey, J.1
-
30
-
-
38649094868
-
The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools
-
Klimek J., Eddes J., Hohmann L., Jackson J., Peterson A., Letarte S., et al. The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools. J Proteome Res 2008, 7:96-103.
-
(2008)
J Proteome Res
, vol.7
, pp. 96-103
-
-
Klimek, J.1
Eddes, J.2
Hohmann, L.3
Jackson, J.4
Peterson, A.5
Letarte, S.6
-
31
-
-
34948874252
-
Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
-
Zhang B., Chambers M., Tabb D. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res 2007, 6:3549-3557.
-
(2007)
J Proteome Res
, vol.6
, pp. 3549-3557
-
-
Zhang, B.1
Chambers, M.2
Tabb, D.3
-
32
-
-
0036406762
-
Experimental protein mixture for validating tandem mass spectral analysis
-
Keller A., Purvine S., Nesvizhskii A., Stolyar S., Goodlett D., Kolker E. Experimental protein mixture for validating tandem mass spectral analysis. OMICS 2002, 6:207-212.
-
(2002)
OMICS
, vol.6
, pp. 207-212
-
-
Keller, A.1
Purvine, S.2
Nesvizhskii, A.3
Stolyar, S.4
Goodlett, D.5
Kolker, E.6
-
33
-
-
46249114017
-
Rapid and accurate peptide identification from tandem mass spectra
-
Park C., Klammer A., Käll L., MacCoss M., Noble W. Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res 2008, 7:3022-3027.
-
(2008)
J Proteome Res
, vol.7
, pp. 3022-3027
-
-
Park, C.1
Klammer, A.2
Käll, L.3
MacCoss, M.4
Noble, W.5
-
34
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng J., McCormack A., Yates J. 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.1
McCormack, A.2
Yates, J.3
-
35
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
Liu H., Sadygov R., Yates J. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004, 76:4193-4201.
-
(2004)
Anal Chem
, vol.76
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.2
Yates, J.3
-
36
-
-
12244270638
-
Differential proteomics via probabilistic peptide identification scores
-
Colinge J., Chiappe D., Lagache S., Moniatte M., Bougueleret L. Differential proteomics via probabilistic peptide identification scores. Anal Chem 2005, 77:596-606.
-
(2005)
Anal Chem
, vol.77
, pp. 596-606
-
-
Colinge, J.1
Chiappe, D.2
Lagache, S.3
Moniatte, M.4
Bougueleret, L.5
-
37
-
-
63549095080
-
Qvality: non-parametric estimation of q-values and posterior error probabilities
-
Käll L., Storey J., Noble W. Qvality: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics 2009, 25:964-966.
-
(2009)
Bioinformatics
, vol.25
, pp. 964-966
-
-
Käll, L.1
Storey, J.2
Noble, W.3
|