-
1
-
-
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. 75, 4646-4658 (2003).
-
(2003)
Anal. Chem
, vol.75
, pp. 4646-4658
-
-
Nesvizhskii, A.I.1
Keller, A.2
Kolker, E.3
Aebersold, R.4
-
2
-
-
31644446949
-
Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition
-
Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P. & Geromanos, S.J. Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 5, 144-156 (2006).
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 144-156
-
-
Silva, J.C.1
Gorenstein, M.V.2
Li, G.Z.3
Vissers, J.P.4
Geromanos, S.J.5
-
3
-
-
0033535961
-
Accurate quantitation of protein expression and site-specific phosphorylation
-
Oda, Y., Huang, K., Cross, F.R., Cowburn, D. & Chait, B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 96, 6591-6596 (1999).
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 6591-6596
-
-
Oda, Y.1
Huang, K.2
Cross, F.R.3
Cowburn, D.4
Chait, B.T.5
-
4
-
-
33644524918
-
Mass spectrometry-based proteomics turns quantitative
-
Ong, S.E. & Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005).
-
(2005)
Nat. Chem. Biol
, vol.1
, pp. 252-262
-
-
Ong, S.E.1
Mann, M.2
-
5
-
-
0036583926
-
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
-
Ong, S.E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386 (2002).
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 376-386
-
-
Ong, S.E.1
-
6
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
Gygi, S.P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 994-999 (1999).
-
(1999)
Nat. Biotechnol
, vol.17
, pp. 994-999
-
-
Gygi, S.P.1
-
7
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W. & Gygri, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 100, 6940-6945 (2003).
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygri, S.P.5
-
8
-
-
22844436250
-
Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards
-
Ishihama, Y. et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 23, 617-621 (2005).
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 617-621
-
-
Ishihama, Y.1
-
9
-
-
3242731195
-
-
Liu, H., Sadygov, R.G. & Yates, J.R. 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201 (2004).
-
Liu, H., Sadygov, R.G. & Yates, J.R. 3rd. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201 (2004).
-
-
-
-
10
-
-
0348142993
-
Changes in the protein expression of yeast as a function of carbon source
-
Gao, J., Opiteck, G.J., Friedrichs, M.S., Dongre, A.R. & Hefta, S.A. Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2, 643-649 (2003).
-
(2003)
J. Proteome Res
, vol.2
, pp. 643-649
-
-
Gao, J.1
Opiteck, G.J.2
Friedrichs, M.S.3
Dongre, A.R.4
Hefta, S.A.5
-
11
-
-
0037015602
-
A proteomic view of the Plasmodium falciparum life cycle
-
Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520-526 (2002).
-
(2002)
Nature
, vol.419
, pp. 520-526
-
-
Florens, L.1
-
12
-
-
23044504789
-
Guidelines for the routine application of the Peptide hits technique
-
Gao, J., Friedrichs, M.S., Dongre, A.R. & Opiteck, G.J. Guidelines for the routine application of the Peptide hits technique. J. Am. Soc. Mass. Spectrom. 16, 1231-1238 (2005).
-
(2005)
J. Am. Soc. Mass. Spectrom
, vol.16
, pp. 1231-1238
-
-
Gao, J.1
Friedrichs, M.S.2
Dongre, A.R.3
Opiteck, G.J.4
-
13
-
-
33644864034
-
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
-
States, D.J. et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24, 333-338 (2006).
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 333-338
-
-
States, D.J.1
-
14
-
-
12144291497
-
Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling
-
Blondeau, F. et al. Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl. Acad. Sci. U.S.A. 101, 3833-3838 (2004).
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, pp. 3833-3838
-
-
Blondeau, F.1
-
15
-
-
33645993265
-
Global survey of organ and organette protein expression in mouse: Combined proteomic and transcriptomic profiling
-
Kislinger, T. et al. Global survey of organ and organette protein expression in mouse: Combined proteomic and transcriptomic profiling. Cell 125, 173-186 (2006).
-
(2006)
Cell
, vol.125
, pp. 173-186
-
-
Kislinger, T.1
-
16
-
-
24944559026
-
Proteome dynamics during C2C12 myoblast differentiation
-
Kislinger, T. et al. Proteome dynamics during C2C12 myoblast differentiation. Mol. Cell Proteomics 4, 887-901 (2005).
-
(2005)
Mol. Cell Proteomics
, vol.4
, pp. 887-901
-
-
Kislinger, T.1
-
17
-
-
0036708081
-
Proteomics goes quantitative: Measuring protein abundance
-
Steen, H. & Pandey, A. Proteomics goes quantitative: Measuring protein abundance. Trends Biotechnol. 20, 361-364 (2002).
-
(2002)
Trends Biotechnol
, vol.20
, pp. 361-364
-
-
Steen, H.1
Pandey, A.2
-
18
-
-
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. & Gygi, S.P. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 22, 214-219 (2004).
-
(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
-
19
-
-
0036808751
-
Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra
-
Gay, S., Binz, P.A., Hochstrasser, D.F. & Appel, R.D. Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra. Proteomics 2, 1374-1391 (2002).
-
(2002)
Proteomics
, vol.2
, pp. 1374-1391
-
-
Gay, S.1
Binz, P.A.2
Hochstrasser, D.F.3
Appel, R.D.4
-
20
-
-
21244443812
-
The use of proteotypic peptide libraries for protein identification
-
Craig, R., Cortens, J.P. & Beavis, R.C. The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass. Spectrom. 19, 1844-1850 (2005).
-
(2005)
Rapid Commun. Mass. Spectrom
, vol.19
, pp. 1844-1850
-
-
Craig, R.1
Cortens, J.P.2
Beavis, R.C.3
-
21
-
-
21744435622
-
Scoring proteomes with proteotypic peptide probes
-
Kuster, B., Schirle, M., Mallick, P. & AebersoLd, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6 577-583 (2005).
-
(2005)
Nat. Rev. Mol. Cell Biol
, vol.6
, pp. 577-583
-
-
Kuster, B.1
Schirle, M.2
Mallick, P.3
AebersoLd, R.4
-
22
-
-
11144334589
-
Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis ofcomptex protein mixtures
-
Le Bihan, T., Robinson, M.D., Stewart, I.I. & Figeys, D. Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis ofcomptex protein mixtures. J. Proteome Res. 3, 1138-1148 (2004).
-
(2004)
J. Proteome Res
, vol.3
, pp. 1138-1148
-
-
Le Bihan, T.1
Robinson, M.D.2
Stewart, I.I.3
Figeys, D.4
-
23
-
-
33846133955
-
Computational prediction of proteotypic peptides for quantitative proteomics
-
Mallick, P. et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (2007).
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 125-131
-
-
Mallick, P.1
-
24
-
-
33747885134
-
A computational approach toward label-free protein quantification using predicted peptide detectability
-
Tang, H. et al. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22, e481-e488 (2006).
-
(2006)
Bioinformatics
, vol.22
-
-
Tang, H.1
-
25
-
-
33846165487
-
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
-
Lu, P., Vogel, C., Wang, R., Yao, X. & Marcotte, E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25, 117-124 (2007).
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 117-124
-
-
Lu, P.1
Vogel, C.2
Wang, R.3
Yao, X.4
Marcotte, E.M.5
-
26
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
-
27
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman, J.R. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846 (2006).
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
-
28
-
-
0032694167
-
A sampling of the yeast proteome
-
Futcher, B., Latter, G.I., Monardo, P., McLaughlin, C.S. & Garrels, J.I. A sampling of the yeast proteome. Mol. Cell. Biol. 19, 7357-7368 (1999).
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 7357-7368
-
-
Futcher, B.1
Latter, G.I.2
Monardo, P.3
McLaughlin, C.S.4
Garrels, J.I.5
-
29
-
-
24044496176
-
Localization, annotation, and comparison of the Escherichia coli K-12 proteome undertwo states of growth
-
Lopez-Campistrous, A. et al. Localization, annotation, and comparison of the Escherichia coli K-12 proteome undertwo states of growth. Mol. Cell Proteomics 4, 1205-1209 (2005).
-
(2005)
Mol. Cell Proteomics
, vol.4
, pp. 1205-1209
-
-
Lopez-Campistrous, A.1
-
30
-
-
33845757588
-
Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome
-
Lu, P. et al. Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metab. Eng. 9, 8-20 (2007).
-
(2007)
Metab. Eng
, vol.9
, pp. 8-20
-
-
Lu, P.1
-
31
-
-
44449097260
-
The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways
-
Wang, R. & Marcotte, E. M. The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways. J. Proteome Res. 7, 855-865 (2008).
-
(2008)
J. Proteome Res
, vol.7
, pp. 855-865
-
-
Wang, R.1
Marcotte, E.M.2
-
32
-
-
44249091879
-
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
-
Baerenfaller, K. et al. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320, 938-941 (2008).
-
(2008)
Science
, vol.320
, pp. 938-941
-
-
Baerenfaller, K.1
-
33
-
-
33847081243
-
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
-
Schmidt, M.W., Houseman, A., Ivanov, A.R. & Wolf, D.A. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe. Mol. Syst. Biol. 3, 79 (2007).
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 79
-
-
Schmidt, M.W.1
Houseman, A.2
Ivanov, A.R.3
Wolf, D.A.4
-
34
-
-
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. 74, 5383-5392 (2002).
-
(2002)
Anal. Chem
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
35
-
-
3042662113
-
In silico proteome analysis to facilitate proteomics experiments using mass spectrometry
-
Cagney, G., Amiri, S., Premawaradena, T., Lindo, M. & Emiti, A. In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci. 1, 5 (2003).
-
(2003)
Proteome Sci
, vol.1
, pp. 5
-
-
Cagney, G.1
Amiri, S.2
Premawaradena, T.3
Lindo, M.4
Emiti, A.5
-
36
-
-
0002437481
-
-
2nd edn. eds. Neidhardt, F.C. et al, ASM Press, Washington, D.C
-
Neidhardt, F.C. & Umbarger, H. E. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 2nd edn. Vol. 1 (eds. Neidhardt, F.C. et al.) 13-16 (ASM Press, Washington, D.C., 1996).
-
(1996)
Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology
, vol.1
, pp. 13-16
-
-
Neidhardt, F.C.1
Umbarger, H.E.2
-
37
-
-
0345863934
-
The CyberCell Database (CCDB): A comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
-
Sundararaj, S. et al. The CyberCell Database (CCDB): A comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 32, D293-D295 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Sundararaj, S.1
-
38
-
-
0032979731
-
Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources
-
Kal, A.J. et al. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol. Biol. Cell 10, 1859-1872 (1999).
-
(1999)
Mol. Biol. Cell
, vol.10
, pp. 1859-1872
-
-
Kal, A.J.1
-
39
-
-
0033828629
-
A quantitative evaluation of SAGE
-
Stollberg, J., Urschitz, U., Urban, Z. & Boyd, C.D. A quantitative evaluation of SAGE. Genome Res. 10, 1241-1248 (2000).
-
(2000)
Genome Res
, vol.10
, pp. 1241-1248
-
-
Stollberg, J.1
Urschitz, U.2
Urban, Z.3
Boyd, C.D.4
-
40
-
-
0028789793
-
Serial analysis of gene expression
-
Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484-487 (1995).
-
(1995)
Science
, vol.270
, pp. 484-487
-
-
Velculescu, V.E.1
Zhang, L.2
Vogelstein, B.3
Kinzler, K.W.4
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