-
1
-
-
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., III (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 III, J.R.3
-
2
-
-
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., and Schieltz, D. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436
-
(1995)
Anal. Chem
, vol.67
, pp. 1426-1436
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
Schieltz, D.4
-
3
-
-
0029645432
-
Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
-
Yates, J. R., III, Eng, J. K., and McCormack, A. L. (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal. Chem. 67, 3202-3210
-
(1995)
Anal. Chem
, vol.67
, pp. 3202-3210
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
-
4
-
-
0033051101
-
Direct analysis of protein complexes using mass spectrometry
-
Link, A. J., Eng, J., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., and Yates, J. R., III (1999) Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682
-
(1999)
Nat. Biotechnol
, vol.17
, pp. 676-682
-
-
Link, A.J.1
Eng, J.2
Schieltz, D.M.3
Carmack, E.4
Mize, G.J.5
Morris, D.R.6
Garvik, B.M.7
Yates III, J.R.8
-
5
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 19, 242-247
-
(2001)
Nat Biotechnol
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates III, J.R.3
-
6
-
-
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., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 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
-
7
-
-
0037015602
-
A proteomic view of the Plasmodium falciparum life cycle
-
Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., Wu, Y., Gardner, M. J., Holder, A. A., Sinden, R. E., Yates, J. R., and Carucci, D. J. (2002) A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520-526
-
(2002)
Nature
, vol.419
, pp. 520-526
-
-
Florens, L.1
Washburn, M.P.2
Raine, J.D.3
Anthony, R.M.4
Grainger, M.5
Haynes, J.D.6
Moch, J.K.7
Muster, N.8
Sacci, J.B.9
Tabb, D.L.10
Witney, A.A.11
Wolters, D.12
Wu, Y.13
Gardner, M.J.14
Holder, A.A.15
Sinden, R.E.16
Yates, J.R.17
Carucci, D.J.18
-
8
-
-
14844360847
-
Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: The human proteome
-
Qian, W. J., Liu, T., Monroe, M. E., Strittmatter, E. F., Jacobs, J. M., Kangas, L. J., Petritis, K., Camp, D. G., II, and Smith, R. D. (2005) Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res. 4, 53-62
-
(2005)
J. Proteome Res
, vol.4
, pp. 53-62
-
-
Qian, W.J.1
Liu, T.2
Monroe, M.E.3
Strittmatter, E.F.4
Jacobs, J.M.5
Kangas, L.J.6
Petritis, K.7
Camp II, D.G.8
Smith, R.D.9
-
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., 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
-
10
-
-
0037953090
-
Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility
-
Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., and Yates, J. R., III (2003) Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75, 2470-2477
-
(2003)
Anal. Chem
, vol.75
, pp. 2470-2477
-
-
Tabb, D.L.1
MacCoss, M.J.2
Wu, C.C.3
Anderson, S.D.4
Yates III, J.R.5
-
11
-
-
0043064042
-
A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
-
Sadygov, R. G., and Yates, J. R., III (2003) A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal. Chem. 75, 3792-3798
-
(2003)
Anal. Chem
, vol.75
, pp. 3792-3798
-
-
Sadygov, R.G.1
Yates III, J.R.2
-
12
-
-
0036209134
-
Qscore: An algorithm for evaluating SEQUEST database search results
-
Moore, R. E., Young, M. K., and Lee, T. D. (2002) Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 13, 378-386
-
(2002)
J. Am. Soc. Mass Spectrom
, vol.13
, pp. 378-386
-
-
Moore, R.E.1
Young, M.K.2
Lee, T.D.3
-
13
-
-
0036828724
-
Probability-based validation of protein identifications using a modified SEQUEST algorithm
-
MacCoss, M. J., Wu, C. C., and Yates, J. R., III (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599
-
(2002)
Anal. Chem
, vol.74
, pp. 5593-5599
-
-
MacCoss, M.J.1
Wu, C.C.2
Yates III, J.R.3
-
14
-
-
0042972838
-
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores
-
Anderson, D. C., Li, W., Payan, D. G., and Noble, W. S. (2003) A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2, 137-146
-
(2003)
J. Proteome Res
, vol.2
, pp. 137-146
-
-
Anderson, D.C.1
Li, W.2
Payan, D.G.3
Noble, W.S.4
-
15
-
-
1842423492
-
A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST
-
Razumovskaya, J., Olman, V., Xu, D., Uberbacher, E. C., VerBerkmoes, N. C., Hettich, R. L., and Xu, Y. (2004) A computational method for assessing peptide-identification reliability in tandem mass spectrometry analysis with SEQUEST. Proteomics 4, 961-969
-
(2004)
Proteomics
, vol.4
, pp. 961-969
-
-
Razumovskaya, J.1
Olman, V.2
Xu, D.3
Uberbacher, E.C.4
VerBerkmoes, N.C.5
Hettich, R.L.6
Xu, Y.7
-
16
-
-
0141585549
-
PRISM, a generic large scale proteomic investigation strategy for mammals
-
Kislinger, T., Rahman, K., Radulovic, D., Cox, B., Rossant, J., and Emili, A. (2003) PRISM, a generic large scale proteomic investigation strategy for mammals. Mol. Cell. Proteomics 2, 96-106
-
(2003)
Mol. Cell. Proteomics
, vol.2
, pp. 96-106
-
-
Kislinger, T.1
Rahman, K.2
Radulovic, D.3
Cox, B.4
Rossant, J.5
Emili, A.6
-
17
-
-
10044248655
-
Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST
-
Lopez-Ferrer, D., Martinez-Bartolome, S., Villar, M., Campillos, M., Martin-Maroto, F., and Vazquez, J. (2004) Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal. Chem. 76, 6853-6860
-
(2004)
Anal. Chem
, vol.76
, pp. 6853-6860
-
-
Lopez-Ferrer, D.1
Martinez-Bartolome, S.2
Villar, M.3
Campillos, M.4
Martin-Maroto, F.5
Vazquez, J.6
-
18
-
-
0035829361
-
Controlling the false discovery rate in behavior genetics research
-
Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav. Brain Res. 125, 279-284
-
(2001)
Behav. Brain Res
, vol.125
, pp. 279-284
-
-
Benjamini, Y.1
Drai, D.2
Elmer, G.3
Kafkafi, N.4
Golani, I.5
-
20
-
-
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
-
21
-
-
0036211823
-
RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
-
Field, H. I., Fenyo, D., and Beavis, R. C. (2002) RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36-47
-
(2002)
Proteomics
, vol.2
, pp. 36-47
-
-
Field, H.I.1
Fenyo, D.2
Beavis, R.C.3
-
22
-
-
0742305695
-
Intensity-based protein identification by machine learning from a library of tandem mass spectra
-
Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., and Gygi, S. P. (2004) Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 214-219
-
-
Elias, J.E.1
Gibbons, F.D.2
King, O.D.3
Roth, F.P.4
Gygi, S.P.5
-
23
-
-
0002451984
-
SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database
-
Bafna, V., and Edwards, N. (2001) SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 17, Suppl. 1, S13-S21
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Bafna, V.1
Edwards, N.2
-
24
-
-
0041358793
-
OLAV: Towards high-throughput tandem mass spectrometry data identification
-
Colinge, J., Masselot, A., Giron, M., Dessingy, T., and Magnin, J. (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463
-
(2003)
Proteomics
, vol.3
, pp. 1454-1463
-
-
Colinge, J.1
Masselot, A.2
Giron, M.3
Dessingy, T.4
Magnin, J.5
-
25
-
-
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
-
26
-
-
3042735333
-
High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
-
Colinge, J., Masselot, A., Cusin, I., Mahe, E., Niknejad, A., Argoud-Puy, G., Reffas, S., Bederr, N., Gleizes, A., Rey, P. A., and Bougueleret, L (2004) High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 4, 1977-1984
-
(2004)
Proteomics
, vol.4
, pp. 1977-1984
-
-
Colinge, J.1
Masselot, A.2
Cusin, I.3
Mahe, E.4
Niknejad, A.5
Argoud-Puy, G.6
Reffas, S.7
Bederr, N.8
Gleizes, A.9
Rey, P.A.10
Bougueleret, L.11
-
27
-
-
0037442649
-
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
-
Fenyo, D., and Beavis, R. C. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768-774
-
(2003)
Anal. Chem
, vol.75
, pp. 768-774
-
-
Fenyo, D.1
Beavis, R.C.2
-
28
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
29
-
-
3042735127
-
The need for guidelines in publication of peptide and protein identification data. Working Group on Publication Guidelines for Peptide and Protein Identification Data
-
Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data. Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol. Cell. Proteomics 3, 531-533
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 531-533
-
-
Carr, S.1
Aebersold, R.2
Baldwin, M.3
Burlingame, A.4
Clauser, K.5
Nesvizhskii, A.6
-
30
-
-
2542640024
-
Protein identification by mass spectrometry. Issues to be considered
-
Baldwin, M. A. (2004) Protein identification by mass spectrometry. Issues to be considered. Mol. Cell. Proteomics 3, 1-9
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 1-9
-
-
Baldwin, M.A.1
-
31
-
-
0037171444
-
Prolactin is a component of the human synovial liquid and modulates the growth and chondrogenic differentiation of bone marrow-derived mesenchymal stem cells
-
Ogueta, S., Munoz, J., Obregon, E., Delgado-Baeza, E., and Garcia-Ruiz, J. P. (2002) Prolactin is a component of the human synovial liquid and modulates the growth and chondrogenic differentiation of bone marrow-derived mesenchymal stem cells. Mol. Cell. Endocrinol. 190, 51-63
-
(2002)
Mol. Cell. Endocrinol
, vol.190
, pp. 51-63
-
-
Ogueta, S.1
Munoz, J.2
Obregon, E.3
Delgado-Baeza, E.4
Garcia-Ruiz, J.P.5
-
32
-
-
33645708138
-
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data. Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
-
Nesvizhskii, A. I., Roos, F. F., Grossmann, J., Vogelzang, M., Eddes, J. S., Gruissem, W., Baginsky, S., and Aebersold, R. (2006) Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data. Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol. Cell. Proteomics 5, 652-670
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 652-670
-
-
Nesvizhskii, A.I.1
Roos, F.F.2
Grossmann, J.3
Vogelzang, M.4
Eddes, J.S.5
Gruissem, W.6
Baginsky, S.7
Aebersold, R.8
-
33
-
-
24744455665
-
Automatic quality assessment of peptide tandem mass spectra
-
Bern, M., Goldberg, D., McDonald, W. H., and Yates, J. R., III (2004) Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 20, Suppl. 1, i49-i54
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Bern, M.1
Goldberg, D.2
McDonald, W.H.3
Yates III, J.R.4
-
34
-
-
4444350538
-
Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry
-
Strittmatter, E. F., Kangas, L. J., Petritis, K., Mottaz, H. M., Anderson, G. A., Shen, Y., Jacobs, J. M., Camp, D. G., II, and Smith, R. D. (2004) Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J. Proteome Res. 3, 760-769
-
(2004)
J. Proteome Res
, vol.3
, pp. 760-769
-
-
Strittmatter, E.F.1
Kangas, L.J.2
Petritis, K.3
Mottaz, H.M.4
Anderson, G.A.5
Shen, Y.6
Jacobs, J.M.7
Camp II, D.G.8
Smith, R.D.9
-
35
-
-
1542617945
-
Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases
-
Sadygov, R. G., Liu, H., and Yates, J. R. (2004) Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 76, 1664-1671
-
(2004)
Anal. Chem
, vol.76
, pp. 1664-1671
-
-
Sadygov, R.G.1
Liu, H.2
Yates, J.R.3
|