-
1
-
-
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
-
-
Steen, H.1
Pandey, A.2
-
2
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn, M.P., Wolters, D. & Yates, J.R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001).
-
(2001)
Nat. Biotechnol
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates III, J.R.3
-
3
-
-
0000312004
-
Protein sequencing by tandem mass spectrometry
-
Hunt, D.F., Yates, J.R., III, Shabanowitz, J., Winston, S. & Hauer, C.R. Protein sequencing by tandem mass spectrometry. Proc. Natl. Acad. Sci. USA 83, 6233-6237 (1986).
-
(1986)
Proc. Natl. Acad. Sci. USA
, vol.83
, pp. 6233-6237
-
-
Hunt, D.F.1
Yates III, J.R.2
Shabanowitz, J.3
Winston, S.4
Hauer, C.R.5
-
4
-
-
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. & Gygi, S.P. 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).
-
(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
-
5
-
-
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
-
6
-
-
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. USA 96, 6591-6596 (1999).
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 6591-6596
-
-
Oda, Y.1
Huang, K.2
Cross, F.R.3
Cowburn, D.4
Chait, B.T.5
-
7
-
-
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
-
8
-
-
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
-
9
-
-
0037795741
-
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
-
Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W. & Gygi, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 100, 6940-6945 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 6940-6945
-
-
Gerber, S.A.1
Rush, J.2
Stemman, O.3
Kirschner, M.W.4
Gygi, S.P.5
-
10
-
-
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
-
11
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
Liu, H., Sadygov, R.G. & Yates, J.R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201 (2004).
-
(2004)
Anal. Chem
, vol.76
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
12
-
-
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
-
13
-
-
26844559000
-
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
-
Ishihama, Y. et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4, 1265-1272 (2005).
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1265-1272
-
-
Ishihama, Y.1
-
14
-
-
0036674269
-
Large-scale proteomic analysis of the human spliceosome
-
Rappsilber, J., Ryder, U., Lamond, A.I. & Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12, 1231-1245 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 1231-1245
-
-
Rappsilber, J.1
Ryder, U.2
Lamond, A.I.3
Mann, M.4
-
15
-
-
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
-
16
-
-
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
-
17
-
-
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
-
18
-
-
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
-
19
-
-
24044496176
-
Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth
-
Lopez-Campistrous, A. et al. Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth. Mol. Cell. Proteomics 4, 1205-1209 (2005).
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1205-1209
-
-
Lopez-Campistrous, A.1
-
20
-
-
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
-
21
-
-
33745220278
-
-
Newman, J.R. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006).
-
Newman, J.R. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006).
-
-
-
-
22
-
-
17944403764
-
Assessing factors for reliable quantitative proteomics based on twodimensional gel electrophoresis
-
Fievet, J. et al. Assessing factors for reliable quantitative proteomics based on twodimensional gel electrophoresis. Proteomics 4, 1939-1949 (2004).
-
(2004)
Proteomics
, vol.4
, pp. 1939-1949
-
-
Fievet, J.1
-
23
-
-
0021997907
-
Elongation factor 1 alpha from Saccharomyces cerevisiae. Rapid largescale purification and molecular characterization
-
Thiele, D. et al. Elongation factor 1 alpha from Saccharomyces cerevisiae. Rapid largescale purification and molecular characterization. J. Biol. Chem. 260, 3084-3089 (1985).
-
(1985)
J. Biol. Chem
, vol.260
, pp. 3084-3089
-
-
Thiele, D.1
-
24
-
-
0141920354
-
-
Greenbaum, D., Colangelo, C., Williams, K. & Gerstein, M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4, 117-117.8 (2003).
-
Greenbaum, D., Colangelo, C., Williams, K. & Gerstein, M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4, 117-117.8 (2003).
-
-
-
-
25
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J. & Doolittle, R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132 (1982).
-
(1982)
J. Mol. Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
26
-
-
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
-
27
-
-
0031442518
-
Characterization of the yeast transcriptome
-
Velculescu, V.E. et al. Characterization of the yeast transcriptome. Cell 88, 243-251 (1997).
-
(1997)
Cell
, vol.88
, pp. 243-251
-
-
Velculescu, V.E.1
-
28
-
-
0013203966
-
FunSpec: A web-based cluster interpreter for yeast
-
Robinson, M.D., Grigull, J., Mohammad, N. & Hughes, T.R. FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3, 35-40 (2002).
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 35-40
-
-
Robinson, M.D.1
Grigull, J.2
Mohammad, N.3
Hughes, T.R.4
-
29
-
-
0034973590
-
Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast
-
Natarajan, K. et al. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21, 4347-4368 (2001).
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 4347-4368
-
-
Natarajan, K.1
-
30
-
-
10744232769
-
Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets
-
Allen, T.E. et al. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J. Bacteriol. 185, 6392-6399 (2003).
-
(2003)
J. Bacteriol
, vol.185
, pp. 6392-6399
-
-
Allen, T.E.1
-
31
-
-
0041923788
-
Toward a protein profile of Escherichia coli: Comparison to its transcription profile
-
Corbin, R.W. et al. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. USA 100, 9232-9237 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9232-9237
-
-
Corbin, R.W.1
-
32
-
-
2342648924
-
Integrating highthroughput and computational data elucidates bacterial networks
-
Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J. & Palsson, B.O. Integrating highthroughput and computational data elucidates bacterial networks. Nature 429, 92-96 (2004).
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.O.5
-
33
-
-
0032567081
-
Dissecting the regulatory circuitry of a eukaryotic genome
-
Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).
-
(1998)
Cell
, vol.95
, pp. 717-728
-
-
Holstege, F.C.1
-
34
-
-
0037197892
-
Precision and functional specificity in mRNA decay
-
Wang, Y. et al. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99, 5860-5865 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5860-5865
-
-
Wang, Y.1
-
35
-
-
10944232800
-
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
-
Beyer, A., Hollunder, J., Nasheuer, H.P. & Wilhelm, T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics 3, 1083-1092 (2004).
-
(2004)
Mol. Cell. Proteomics
, vol.3
, pp. 1083-1092
-
-
Beyer, A.1
Hollunder, J.2
Nasheuer, H.P.3
Wilhelm, T.4
-
36
-
-
0037453060
-
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae
-
Washburn, M.P. et al. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 3107-3112 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3107-3112
-
-
Washburn, M.P.1
-
37
-
-
0036545614
-
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
-
Griffin, T.J. et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1, 323-333 (2002).
-
(2002)
Mol. Cell. Proteomics
, vol.1
, pp. 323-333
-
-
Griffin, T.J.1
-
38
-
-
0033621393
-
Post-translational regulation of Adr1 activity is mediated by its DNA binding domain
-
Sloan, J.S., Dombek, K.M. & Young, E.T. Post-translational regulation of Adr1 activity is mediated by its DNA binding domain. J. Biol. Chem. 274, 37575-37582 (1999).
-
(1999)
J. Biol. Chem
, vol.274
, pp. 37575-37582
-
-
Sloan, J.S.1
Dombek, K.M.2
Young, E.T.3
-
39
-
-
0023038433
-
The ILV5 gene of Saccharomyces cerevisiae is highly expressed
-
Petersen, J.G. & Holmberg, S. The ILV5 gene of Saccharomyces cerevisiae is highly expressed. Nucleic Acids Res. 14, 9631-9651 (1986).
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 9631-9651
-
-
Petersen, J.G.1
Holmberg, S.2
-
40
-
-
0023975739
-
Regulation of isoleucine-valine biosynthesis in Saccharomyces cerevisiae
-
Holmberg, S. & Petersen, J.G. Regulation of isoleucine-valine biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 13, 207-217 (1988).
-
(1988)
Curr. Genet
, vol.13
, pp. 207-217
-
-
Holmberg, S.1
Petersen, J.G.2
-
41
-
-
0023659507
-
The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression
-
Werner, M., Feller, A., Messenguy, F. & Pierard, A. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression. Cell 49, 805-813 (1987).
-
(1987)
Cell
, vol.49
, pp. 805-813
-
-
Werner, M.1
Feller, A.2
Messenguy, F.3
Pierard, A.4
-
42
-
-
1842424944
-
The need for a public proteomics repository
-
Prince, J.T., Carlson, M.W., Wang, R., Lu, P. & Marcotte, E.M. The need for a public proteomics repository. Nat. Biotechnol. 22, 471-472 (2004).
-
(2004)
Nat. Biotechnol
, vol.22
, pp. 471-472
-
-
Prince, J.T.1
Carlson, M.W.2
Wang, R.3
Lu, P.4
Marcotte, E.M.5
-
43
-
-
0037388094
-
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
-
Arava, Y. et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 3889-3894 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
-
44
-
-
21044441648
-
Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis
-
Allemeersch, J. et al. Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis. Plant Physiol. 137, 588-601 (2005).
-
(2005)
Plant Physiol
, vol.137
, pp. 588-601
-
-
Allemeersch, J.1
-
45
-
-
33748377124
-
Quantification of protein half-lives in the budding yeast proteome
-
Belle, A., Tanay, A., Bitincka, L., Shamir, R. & O'Shea, E.K. Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. USA 103, 13004-13009 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 13004-13009
-
-
Belle, A.1
Tanay, A.2
Bitincka, L.3
Shamir, R.4
O'Shea, E.K.5
-
46
-
-
0022971952
-
Amino acid sequences common to rapidly degraded proteins: The PEST hypothesis
-
Rogers, S., Wells, R. & Rechsteiner, M. Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis. Science 234, 364-368 (1986).
-
(1986)
Science
, vol.234
, pp. 364-368
-
-
Rogers, S.1
Wells, R.2
Rechsteiner, M.3
-
47
-
-
0023003380
-
In vivo half-life of a protein is a function of its amino-terminal residue
-
Bachmair, A., Finley, D. & Varshavsky, A. In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179-186 (1986).
-
(1986)
Science
, vol.234
, pp. 179-186
-
-
Bachmair, A.1
Finley, D.2
Varshavsky, A.3
-
48
-
-
0002437481
-
-
edn. 2, eds. Neidhardt, F.C. et al, ASM Press, Washington, DC
-
Neidhardt, F.C. & Umbarger, H.E. in Escherichia coli and Salmonella Typhimurium: Cellular and Molecular Biology, edn. 2, vol. 1 (eds. Neidhardt, F.C. et al.) 13-16 (ASM Press, Washington, DC, 1996).
-
(1996)
Escherichia coli and Salmonella Typhimurium: Cellular and Molecular Biology
, vol.1
, pp. 13-16
-
-
Neidhardt, F.C.1
Umbarger, H.E.2
-
49
-
-
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
-
50
-
-
0036747350
-
Approaching complete peroxisome characterization by gas-phase fractionation
-
Yi, E.C. et al. Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis 23, 3205-3216 (2002).
-
(2002)
Electrophoresis
, vol.23
, pp. 3205-3216
-
-
Yi, E.C.1
|