-
1
-
-
0037435030
-
Mass spectrometry-based proteomics
-
DOI 10.1038/nature01511
-
Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (6928), 198-207. (Pubitemid 36362757)
-
(2003)
Nature
, vol.422
, Issue.6928
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
2
-
-
0000857494
-
-
Eng, J. K.; McCormack, A. L.; Yates, J. R., III. 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 III, J.R.3
-
3
-
-
0028575316
-
Error-tolerant identification of peptides in sequence databases by peptide sequence tags
-
Mann, M.; Wilm, M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66 (24), 4390-4399. (Pubitemid 124006101)
-
(1994)
Analytical Chemistry
, vol.66
, Issue.24
, pp. 4390-4399
-
-
Mann, M.1
Wilm, M.2
-
4
-
-
0033434080
-
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 (18), 3551-3567. (Pubitemid 30007252)
-
(1999)
Electrophoresis
, vol.20
, Issue.18
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.C.2
Creasy, D.M.3
Cottrell, J.S.4
-
5
-
-
0036211823
-
RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
-
DOI 10.1002/1615-9861(200201)2:1<36::AID-PROT36>3.0.CO;2-W
-
Field, H. I.; Fenyo, D.; Beavis, R. C. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2002, 2 (1), 36-47. (Pubitemid 34273097)
-
(2002)
Proteomics
, vol.2
, Issue.1
, pp. 36-47
-
-
Field, H.I.1
Fenyo, D.2
Beavis, R.C.3
-
6
-
-
0036808207
-
ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data
-
DOI 10.1002/1615-9861(200210)2:10<1406::AID-PROT1406>3.0.CO;2-9
-
Zhang, N.; Aebersold, R.; Schwikowski, B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2002, 2 (10), 1406-1412. (Pubitemid 35340021)
-
(2002)
Proteomics
, vol.2
, Issue.10
, pp. 1406-1412
-
-
Zhang, N.1
Aebersold, R.2
Schwikowski, B.3
-
7
-
-
0038047148
-
Popitam: Towards new heuristic strategies to improve protein identification from tandem mass spectrometry data
-
DOI 10.1002/pmic.200300402
-
Hernandez, P.; Gras, R.; Frey, J.; Appel, R. D. Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics 2003, 3 (6), 870-878. (Pubitemid 36801673)
-
(2003)
Proteomics
, vol.3
, Issue.6
, pp. 870-878
-
-
Hernandez, P.1
Gras, R.2
Frey, J.3
Appel, R.D.4
-
8
-
-
0141955057
-
A method for reducing the time required to match protein sequences with tandem mass spectra
-
Craig, R.; Beavis, R. C. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 2003, 17 (20), 2310-2316. (Pubitemid 37243315)
-
(2003)
Rapid Communications in Mass Spectrometry
, vol.17
, Issue.20
, pp. 2310-2316
-
-
Craig, R.1
Beavis, R.C.2
-
9
-
-
3042733910
-
2+ in Schizosaccharomyces pombe through amino acid-coded mass tagging and liquid chromatography tandem mass spectrometry
-
DOI 10.1074/mcp.M300122-MCP200
-
Bae, W.; Chen, X. Proteomic study for the cellular responses to Cd2+ in Schizosaccharomyces pombe through amino acid-coded mass tagging and liquid chromatography tandem mass spectrometry. Mol. Cell. Proteomics 2004, 3 (6), 596-607. (Pubitemid 38878519)
-
(2004)
Molecular and Cellular Proteomics
, vol.3
, Issue.6
, pp. 596-607
-
-
Bae, W.1
Chen, X.2
-
10
-
-
26844556166
-
I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions
-
DOI 10.1021/pr050225e
-
Tackett, A. J.; DeGrasse, J. A.; Sekedat, M. D.; Oeffinger, M.; Rout, M. P.; Chait, B. T. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Proteome Res. 2005, 4 (5), 1752-1756. (Pubitemid 41464803)
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.5
, pp. 1752-1756
-
-
Tackett, A.J.1
Degrasse, J.A.2
Sekedat, M.D.3
Oeffinger, M.4
Rout, M.P.5
Chait, B.T.6
-
11
-
-
0029644596
-
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
-
Yates, J. R., III; Eng, J. K.; McCormack, A. L.; Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 1995, 67 (8), 1426-1436.
-
(1995)
Anal. Chem.
, vol.67
, Issue.8
, pp. 1426-1436
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
Schieltz, D.4
-
12
-
-
0035107717
-
Efficiency of database search for identification of mutated and modified proteins via mass spectrometry
-
DOI 10.1101/gr.154101
-
Pevzner, P. A.; Mulyukov, Z.; Dancik, V.; Tang, C. L. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. 2001, 11 (2), 290-299. (Pubitemid 32166538)
-
(2001)
Genome Research
, vol.11
, Issue.2
, pp. 290-299
-
-
Pevzner, P.A.1
Mulyukov, Z.2
Dancik, V.3
Tang, C.L.4
-
13
-
-
0036138754
-
Peptide sequence motif analysis of tandem MS data with the SALSA Algorithm
-
DOI 10.1021/ac0155512
-
Liebler, D. C.; Hansen, B. T.; Davey, S. W.; Tiscareno, L.; Mason, D. E. Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal. Chem. 2002, 74 (1), 203-210. (Pubitemid 34044445)
-
(2002)
Analytical Chemistry
, vol.74
, Issue.1
, pp. 203-210
-
-
Liebler, D.C.1
Hansen, B.T.2
Davey, S.W.3
Tiscareno, L.4
Mason, D.E.5
-
14
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
DOI 10.1038/13690
-
Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17 (10), 994-999. (Pubitemid 29474856)
-
(1999)
Nature Biotechnology
, vol.17
, Issue.10
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
15
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1 (5), 376-386.
-
(2002)
Mol. Cell. Proteomics
, vol.1
, Issue.5
, pp. 376-386
-
-
Ong, S.E.1
Blagoev, B.2
Kratchmarova, I.3
Kristensen, D.B.4
Steen, H.5
Pandey, A.6
-
16
-
-
0036828724
-
Probability based validation of protein identifications using a modified SEQUEST algorithm
-
DOI 10.1021/ac025826t
-
MacCoss, M. J.; Wu, C. C.; Yates, J. R. 3rd, Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 2002, 74 (21), 5593-5599 (Pubitemid 35253125)
-
(2002)
Analytical Chemistry
, vol.74
, Issue.21
, pp. 5593-5599
-
-
MacCoss, M.J.1
Wu, C.C.2
Yates III, J.R.3
-
17
-
-
0034161650
-
A statistical basis for testing the significance of mass spectrometric protein identification results
-
DOI 10.1021/ac990792j
-
Eriksson, J.; Chait, B. T.; Fenyo, D. A statistical basis for testing the significance of mass spectrometric protein identification results. Anal. Chem. 2000, 72 (5), 999-1005. (Pubitemid 30127407)
-
(2000)
Analytical Chemistry
, vol.72
, Issue.5
, pp. 999-1005
-
-
Eriksson, J.1
Chait, B.T.2
Fenyo, D.3
-
18
-
-
0036206553
-
A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis
-
DOI 10.1002/1615-9861(200203)2:3<262::AID-PROT262>3.0.CO;2-W
-
Eriksson, J.; Fenyo, D. A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis. Proteomics 2002, 2 (3), 262-270. (Pubitemid 34269980)
-
(2002)
Proteomics
, vol.2
, Issue.3
, pp. 262-270
-
-
Eriksson, J.1
Fenyo, D.2
-
19
-
-
1242307292
-
Probity: A Protein Identification Algorithm with Accurate Assignment of the Statistical Significance of the Results
-
DOI 10.1021/pr034048y
-
Eriksson, J.; Fenyo, D. Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results. J. Proteome Res. 2004, 3 (1), 32-36. (Pubitemid 38233447)
-
(2004)
Journal of Proteome Research
, vol.3
, Issue.1
, pp. 32-36
-
-
Eriksson, J.1
Fenyo, D.2
-
20
-
-
3042737683
-
Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics
-
DOI 10.1021/ac035229m
-
Resing, K. A.; Meyer-Arendt, K.; Mendoza, A. M.; Aveline-Wolf, L. D.; Jonscher, K. R.; Pierce, K. G.; Old, W. M.; Cheung, H. T.; Russell, S.; Wattawa, J. L.; Goehle, G. R.; Knight, R. D.; Ahn, N. G. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 2004, 76 (13), 3556-3568. (Pubitemid 38868816)
-
(2004)
Analytical Chemistry
, vol.76
, Issue.13
, pp. 3556-3568
-
-
Resing, K.A.1
Meyer-Arendt, K.2
Mendoza, A.M.3
Aveline-Wolf, L.D.4
Jonscher, K.R.5
Pierce, K.G.6
Old, W.M.7
Cheung, H.T.8
Russell, S.9
Wattawa, J.L.10
Goehle, G.R.11
Knight, R.D.12
Ahn, N.G.13
-
21
-
-
0036209134
-
Qscore: An algorithm for evaluating SEQUEST database search results
-
DOI 10.1016/S1044-0305(02)00352-5, PII S1044030502003525
-
Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 2002, 13 (4), 378-386. (Pubitemid 34280088)
-
(2002)
Journal of the American Society for Mass Spectrometry
, vol.13
, Issue.4
, pp. 378-386
-
-
Moore, R.E.1
Young, M.K.2
Lee, T.D.3
-
22
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
DOI 10.1021/ac025747h
-
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 (20), 5383-5392. (Pubitemid 35215372)
-
(2002)
Analytical Chemistry
, vol.74
, Issue.20
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
23
-
-
0742305695
-
Intensity-based protein identification by machine learning from a library of tandem mass spectra
-
DOI 10.1038/nbt930
-
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 (2), 214-219. (Pubitemid 38160538)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.2
, pp. 214-219
-
-
Elias, J.E.1
Gibbons, F.D.2
King, O.D.3
Roth, F.P.4
Gygi, S.P.5
-
24
-
-
38649083116
-
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling
-
DOI 10.1021/pr7006818
-
Choi, H.; Ghosh, D.; Nesvizhskii, A. I. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteome Res. 2008, 7 (1), 286-292. (Pubitemid 351171141)
-
(2008)
Journal of Proteome Research
, vol.7
, Issue.1
, pp. 286-292
-
-
Choi, H.1
Ghosh, D.2
Nesvizhskii, A.I.3
-
25
-
-
20844457100
-
Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra
-
DOI 10.1021/pr049754t
-
Chen, Y.; Kwon, S. W.; Kim, S. C.; Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J. Proteome Res. 2005, 4 (3), 998-1005. (Pubitemid 40863290)
-
(2005)
Journal of Proteome Research
, vol.4
, Issue.3
, pp. 998-1005
-
-
Chen, Y.1
Kwon, S.W.2
Kim, S.C.3
Zhao, Y.4
-
26
-
-
35848970747
-
Mapping protein post-translational modifications with mass spectrometry
-
DOI 10.1038/nmeth1100, PII NMETH1100
-
Witze, E. S.; Old, W. M.; Resing, K. A.; Ahn, N. G. Mapping protein post-translational modifications with mass spectrometry. Nat. Methods 2007, 4 (10), 798-806. (Pubitemid 350055576)
-
(2007)
Nature Methods
, vol.4
, Issue.10
, pp. 798-806
-
-
Witze, E.S.1
Old, W.M.2
Resing, K.A.3
Ahn, N.G.4
-
27
-
-
44449117052
-
Identification and validation of eukaryotic aspartate and glutamate methylation in proteins
-
Sprung, R.; Chen, Y.; Zhang, K.; Cheng, D.; Zhang, T.; Peng, J.; Zhao, Y. Identification and validation of eukaryotic aspartate and glutamate methylation in proteins. J. Proteome Res. 2008, 7 (3), 1001-1006.
-
(2008)
J. Proteome Res.
, vol.7
, Issue.3
, pp. 1001-1006
-
-
Sprung, R.1
Chen, Y.2
Zhang, K.3
Cheng, D.4
Zhang, T.5
Peng, J.6
Zhao, Y.7
-
28
-
-
33646903914
-
ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures
-
DOI 10.1074/mcp.T500034-MCP200
-
Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures. Mol. Cell. Proteomics 2006, 5 (5), 935-948. (Pubitemid 43792802)
-
(2006)
Molecular and Cellular Proteomics
, vol.5
, Issue.5
, pp. 935-948
-
-
Savitski, M.M.1
Nielsen, M.L.2
Zubarev, R.A.3
|