-
1
-
-
33645813378
-
Mass spectrometry and protein analysis
-
Domon, B., and Aebersold, R. (2006) Mass spectrometry and protein analysis. Science 312, 212-217
-
(2006)
Science
, vol.312
, pp. 212-217
-
-
Domon, B.1
Aebersold, R.2
-
2
-
-
34547176285
-
Proteomics data validation: Why all must provide data
-
Martens, L., and Hermjakob, H. (2007) Proteomics data validation: why all must provide data. Mol. Biosyst. 3, 518-522
-
(2007)
Mol. Biosyst
, vol.3
, pp. 518-522
-
-
Martens, L.1
Hermjakob, H.2
-
3
-
-
34548396821
-
Methods, algorithms and tools in computational proteomics: A practical point of view
-
Matthiesen, R. (2007) Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics 7, 2815-2832
-
(2007)
Proteomics
, vol.7
, pp. 2815-2832
-
-
Matthiesen, R.1
-
4
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J. K., McCormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 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
-
5
-
-
0033434080
-
Probability-based protein identification by searching sequence data-bases using mass spectrometry data
-
Perkins, D. N., Pappin, D. J., Cressy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence data-bases using mass spectrometry data. Electrophoresis 20, 3551-3567
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Cressy, D.M.3
Cottrell, J.S.4
-
6
-
-
11144320641
-
Open source system for analyzing, validating, and storing protein identification data
-
Craig, R., Cortens, J. P., and Beavis, R. C. (2004) Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 3, 1234-1242
-
(2004)
J. Proteome Res
, vol.3
, pp. 1234-1242
-
-
Craig, R.1
Cortens, J.P.2
Beavis, R.C.3
-
7
-
-
29144535689
-
VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins
-
Matthiesen, R., Trelle, M. B., Hojrup, P., Bunkenborg, J., and Jensen, O. N. (2005) VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J. Proteome Res. 4, 2338-2347
-
(2005)
J. Proteome Res
, vol.4
, pp. 2338-2347
-
-
Matthiesen, R.1
Trelle, M.B.2
Hojrup, P.3
Bunkenborg, J.4
Jensen, O.N.5
-
8
-
-
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
-
9
-
-
18744398125
-
Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book
-
Sadygov, R. G., Cociorva, D., and Yates, J. R., III (2004) Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat Methods 1, 195-202
-
(2004)
Nat Methods
, vol.1
, pp. 195-202
-
-
Sadygov, R.G.1
Cociorva, D.2
Yates III, J.R.3
-
10
-
-
43849101253
-
Comparison of mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted mascot threshold
-
Brosch, M., Swamy, S., Hubbard, T., and Choudhary, J. (2008) Comparison of mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted mascot threshold. Mol. Cell. Proteomics 7, 962-970
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 962-970
-
-
Brosch, M.1
Swamy, S.2
Hubbard, T.3
Choudhary, J.4
-
11
-
-
3142729873
-
RScore: A peptide randomicity score for evaluating tandem mass spectra
-
Li, F., Sun, W., Gao, Y., and Wang, J. (2004) RScore: a peptide randomicity score for evaluating tandem mass spectra. Rapid Commun. Mass Spectrom. 18, 1655-1659
-
(2004)
Rapid Commun. Mass Spectrom
, vol.18
, pp. 1655-1659
-
-
Li, F.1
Sun, W.2
Gao, Y.3
Wang, J.4
-
12
-
-
24044508863
-
New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques
-
Savitski, M. M., Nielsen, M. L., and Zubarev, R. A. (2005) New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques. Mol. Cell. Proteomics 4, 1180-1188
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1180-1188
-
-
Savitski, M.M.1
Nielsen, M.L.2
Zubarev, R.A.3
-
13
-
-
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., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
-
(2002)
Anal. Chem
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
14
-
-
33745218278
-
Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry
-
Zhan, X., and Desiderio, D. M. (2006) Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry. Anal. Biochem. 354, 279-289
-
(2006)
Anal. Biochem
, vol.354
, pp. 279-289
-
-
Zhan, X.1
Desiderio, D.M.2
-
15
-
-
43849104641
-
Targets of tyrosine nitration in diabetic rat retina
-
Zhan, X., Du, Y., Crabb, J. S., Gu, X., Kem, T. S., and Crabb, J. W. (2008) Targets of tyrosine nitration in diabetic rat retina. Mol. Cell. Proteomics 7, 864-874
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 864-874
-
-
Zhan, X.1
Du, Y.2
Crabb, J.S.3
Gu, X.4
Kem, T.S.5
Crabb, J.W.6
-
16
-
-
2442542310
-
Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli
-
Hardwidge, P. R., Rodriguez-Escudero, I., Goode, D., Donohoe, S., Eng, J., Goodlett, D. R., Aebersold, R., and Finlay, B. B. (2004) Proteomic analysis of the intestinal epithelial cell response to enteropathogenic Escherichia coli. J. Biol. Chem. 279, 20127-20136
-
(2004)
J. Biol. Chem
, vol.279
, pp. 20127-20136
-
-
Hardwidge, P.R.1
Rodriguez-Escudero, I.2
Goode, D.3
Donohoe, S.4
Eng, J.5
Goodlett, D.R.6
Aebersold, R.7
Finlay, B.B.8
-
17
-
-
16644362015
-
What to do with "one-hit wonders"?
-
Veenstra, T. D., Conrads, T. P., and Issaq, H. J. (2004) What to do with "one-hit wonders"? Electrophoresis 25, 1278-1279
-
(2004)
Electrophoresis
, vol.25
, pp. 1278-1279
-
-
Veenstra, T.D.1
Conrads, T.P.2
Issaq, H.J.3
-
18
-
-
0036745397
-
CHOMPER: A bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies
-
Eddes, J. S., Kapp, E. A., Frecklington, D. F., Connolly, L. M., Layton, M. J., Moritz, R. L., and Simpson, R. J. (2002) CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies. Proteomics 2, 1097-1103
-
(2002)
Proteomics
, vol.2
, pp. 1097-1103
-
-
Eddes, J.S.1
Kapp, E.A.2
Frecklington, D.F.3
Connolly, L.M.4
Layton, M.J.5
Moritz, R.L.6
Simpson, R.J.7
-
19
-
-
0036393898
-
DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
-
Tabb, D. L., McDonald, W. H., and Yates, J. R., III (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26
-
(2002)
J. Proteome Res
, vol.1
, pp. 21-26
-
-
Tabb, D.L.1
McDonald, W.H.2
Yates III, J.R.3
-
20
-
-
34547907397
-
myProMS, a web server for management and validation of mass spectrometry-based proteomic data
-
Poullet, P., Carpentier, S., and Barillot, E. (2007) myProMS, a web server for management and validation of mass spectrometry-based proteomic data. Proteomics 7, 2553-2556
-
(2007)
Proteomics
, vol.7
, pp. 2553-2556
-
-
Poullet, P.1
Carpentier, S.2
Barillot, E.3
-
21
-
-
38649125220
-
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics
-
Choi, H., and Nesvizhskii, A. I. (2008) Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. J. Proteome Res. 7, 254-265
-
(2008)
J. Proteome Res
, vol.7
, pp. 254-265
-
-
Choi, H.1
Nesvizhskii, A.I.2
-
22
-
-
34548400394
-
A la carte proteomics with an emphasis on gel-free techniques
-
Gevaert, K., Van Damme, P., Ghesquiere, B., Impens, F., Martens, L., Helsens, K., and Vandekerckhove, J. (2007) A la carte proteomics with an emphasis on gel-free techniques. Proteomics 7, 2698-2718
-
(2007)
Proteomics
, vol.7
, pp. 2698-2718
-
-
Gevaert, K.1
Van Damme, P.2
Ghesquiere, B.3
Impens, F.4
Martens, L.5
Helsens, K.6
Vandekerckhove, J.7
-
23
-
-
35348863892
-
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites
-
Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R., and Domon, B. (2007) High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 6, 1809-1817
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1809-1817
-
-
Stahl-Zeng, J.1
Lange, V.2
Ossola, R.3
Eckhardt, K.4
Krek, W.5
Aebersold, R.6
Domon, B.7
-
24
-
-
42049084149
-
Improved recovery of proteome-informative, protein N-terminal peptides; by combined fractional diagonal chromatography (COFRADIC)
-
Staes, A., Van Damme, P., Helsens, K., Demol, H., Vandekerckhove, J., and Gevaert, K. (2008) Improved recovery of proteome-informative, protein N-terminal peptides; by combined fractional diagonal chromatography (COFRADIC). Proteomics 8, 1362-1370
-
(2008)
Proteomics
, vol.8
, pp. 1362-1370
-
-
Staes, A.1
Van Damme, P.2
Helsens, K.3
Demol, H.4
Vandekerckhove, J.5
Gevaert, K.6
-
25
-
-
24144468009
-
Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics?
-
Gevaert, K., Van Damme, P., Martens, L., and Vandekerckhove, J. (2005) Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? Anal. Biochem. 345, 18-29
-
(2005)
Anal. Biochem
, vol.345
, pp. 18-29
-
-
Gevaert, K.1
Van Damme, P.2
Martens, L.3
Vandekerckhove, J.4
-
26
-
-
34447569354
-
Assessing a novel microfluidic interface for shotgun proteome analyses
-
Staes, A., Timmerman, E., Van Damme, J., Helsens, K., Vandekerckhove, J., Vollmer, M., and Gevaert, K. (2007) Assessing a novel microfluidic interface for shotgun proteome analyses. J. Sep. Sci. 30, 1468-1476
-
(2007)
J. Sep. Sci
, vol.30
, pp. 1468-1476
-
-
Staes, A.1
Timmerman, E.2
Van Damme, J.3
Helsens, K.4
Vandekerckhove, J.5
Vollmer, M.6
Gevaert, K.7
-
27
-
-
24144480557
-
DBToolkit: Processing protein databases for peptide-centric proteomics
-
Martens, L., Vandekerckhove, J., and Gevaert, K. (2005) DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (Oxf.) 21, 3584-3585
-
(2005)
Bioinformatics (Oxf.)
, vol.21
, pp. 3584-3585
-
-
Martens, L.1
Vandekerckhove, J.2
Gevaert, K.3
-
28
-
-
23944526367
-
PRIDE: The proteomics identifications database
-
Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545
-
(2005)
Proteomics
, vol.5
, pp. 3537-3545
-
-
Martens, L.1
Hermjakob, H.2
Jones, P.3
Adamski, M.4
Taylor, C.5
States, D.6
Gevaert, K.7
Vandekerckhove, J.8
Apweiler, R.9
-
29
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
-
(2007)
Nat. Methods
, vol.4
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
30
-
-
33847104994
-
MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results
-
Helsens, K., Martens, L., Vandekerckhove, J., and Gevaert, K. (2007) MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results. Proteomics 7, 364-366
-
(2007)
Proteomics
, vol.7
, pp. 364-366
-
-
Helsens, K.1
Martens, L.2
Vandekerckhove, J.3
Gevaert, K.4
-
31
-
-
49049106826
-
LIMS and the art of MS proteomics
-
Piggee, C. (2008) LIMS and the art of MS proteomics. Anal. Chem. 80, 4801-4806
-
(2008)
Anal. Chem
, vol.80
, pp. 4801-4806
-
-
Piggee, C.1
-
32
-
-
0003957032
-
-
2nd Ed, Morgan Kaufmann, San Francisco
-
Ian, H. W., and Eibe, F. (2005) Data Mining. Practical Machine Learning Tools and Techniques, 2nd Ed., Morgan Kaufmann, San Francisco
-
(2005)
Data Mining. Practical Machine Learning Tools and Techniques
-
-
Ian, H.W.1
Eibe, F.2
-
33
-
-
27644555055
-
Interpretation of shotgun proteomic data: The protein inference problem
-
Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
34
-
-
0242653718
-
-
Kapp, E. A., Schutz, F., Reid, G. E., Eddes, J. S., Moritz, R. L., 0'Hair, R. A., Speed, T. P., and Simpson, R. J. (2003) Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 75, 6251-6264
-
Kapp, E. A., Schutz, F., Reid, G. E., Eddes, J. S., Moritz, R. L., 0'Hair, R. A., Speed, T. P., and Simpson, R. J. (2003) Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 75, 6251-6264
-
-
-
-
35
-
-
34548449808
-
Verification of automated peptide identifications from proteomic tandem mass spectra
-
Tabb, D. L., Friedman, D. B., and Ham, A. J. (2006) Verification of automated peptide identifications from proteomic tandem mass spectra. Nat. Protoc. 1, 2213-2222
-
(2006)
Nat. Protoc
, vol.1
, pp. 2213-2222
-
-
Tabb, D.L.1
Friedman, D.B.2
Ham, A.J.3
|