-
1
-
-
20444383859
-
Protein phosphorylation in signaling - 50 Years and counting
-
DOI 10.1016/j.tibs.2005.04.013, PII S0968000405001210, Celebrating 50 Years of the IUBMB
-
Pawson, T., and Scott, J. D. (2005) Protein phosphorylation in signaling-50 years and counting. Trends Biochem. Sci. 30, 286-290 (Pubitemid 40799044)
-
(2005)
Trends in Biochemical Sciences
, vol.30
, Issue.6
, pp. 286-290
-
-
Pawson, T.1
Scott, J.D.2
-
2
-
-
67649213067
-
Phosphopeptide fragmentation and analysis by mass spectrometry
-
Boersema, P. J., Mohammed, S., and Heck, A. J. (2009) Phosphopeptide fragmentation and analysis by mass spectrometry. J. Mass Spectrom. 44, 861-878
-
(2009)
J. Mass Spectrom.
, vol.44
, pp. 861-878
-
-
Boersema, P.J.1
Mohammed, S.2
Heck, A.J.3
-
3
-
-
75749101460
-
Phosphoproteomics for the masses
-
Grimsrud, P. A., Swaney, D. L., Wenger, C. D., Beauchene, N. A., and Coon, J. J. (2010) Phosphoproteomics for the masses. ACS Chem. Biol. 5, 105-119
-
(2010)
ACS Chem. Biol.
, vol.5
, pp. 105-119
-
-
Grimsrud, P.A.1
Swaney, D.L.2
Wenger, C.D.3
Beauchene, N.A.4
Coon, J.J.5
-
4
-
-
34247583996
-
Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins
-
DOI 10.1038/nature05815, PII NATURE05815
-
Hart, G. W., Housley, M. P., and Slawson, C. (2007) Cycling of O-linked beta-N-acetylglucosamine on nucleocytoplasmic proteins. Nature 446, 1017-1022 (Pubitemid 46676063)
-
(2007)
Nature
, vol.446
, Issue.7139
, pp. 1017-1022
-
-
Hart, G.W.1
Housley, M.P.2
Slawson, C.3
-
5
-
-
56349155647
-
Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins
-
Rathert, P., Dhayalan, A., Ma, H., and Jeltsch, A. (2008) Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins. Mol. Biosyst. 4, 1186-1190
-
(2008)
Mol. Biosyst.
, vol.4
, pp. 1186-1190
-
-
Rathert, P.1
Dhayalan, A.2
Ma, H.3
Jeltsch, A.4
-
6
-
-
77149148756
-
Regulation of cellular metabolism by protein lysine acetylation
-
Zhao, S., Xu, W., Jiang, W., Yu, W., Lin, Y., Zhang, T., Yao, J., Zhou, L., Zeng, Y., Li, H., Li, Y., Shi, J., An, W., Hancock, S. M., He, F., Qin, L., Chin, J., Yang, P., Chen, X., Lei, Q., Xiong, Y., and Guan, K. L. (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000-1004
-
(2010)
Science
, vol.327
, pp. 1000-1004
-
-
Zhao, S.1
Xu, W.2
Jiang, W.3
Yu, W.4
Lin, Y.5
Zhang, T.6
Yao, J.7
Zhou, L.8
Zeng, Y.9
Li, H.10
Li, Y.11
Shi, J.12
An, W.13
Hancock, S.M.14
He, F.15
Qin, L.16
Chin, J.17
Yang, P.18
Chen, X.19
Lei, Q.20
Xiong, Y.21
Guan, K.L.22
more..
-
7
-
-
23144452492
-
Weighing in on ubiquitin: The expanding role of mass-spectrometry-based proteomics
-
DOI 10.1038/ncb0805-750
-
Kirkpatrick, D. S., Denison, C., and Gygi, S. P. (2005) Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat. Cell Biol. 7, 750-757 (Pubitemid 41079043)
-
(2005)
Nature Cell Biology
, vol.7
, Issue.8
, pp. 750-757
-
-
Kirkpatrick, D.S.1
Denison, C.2
Gygi, S.P.3
-
8
-
-
0034610814
-
The language of covalent histone modifications
-
DOI 10.1038/47412
-
Strahl, B. D., and Allis, C. D. (2000) The language of covalent histone modifications. Nature 403, 41-45 (Pubitemid 30038513)
-
(2000)
Nature
, vol.403
, Issue.6765
, pp. 41-45
-
-
Strahl, B.D.1
Allis, C.D.2
-
9
-
-
72449187655
-
The intersections between O-GlcNAcylation and phosphorylation: Implications for multiple signaling pathways
-
Zeidan, Q., and Hart, G. W. (2010) The intersections between O-GlcNAcylation and phosphorylation: implications for multiple signaling pathways. J. Cell Sci. 123, 13-22
-
(2010)
J. Cell Sci.
, vol.123
, pp. 13-22
-
-
Zeidan, Q.1
Hart, G.W.2
-
10
-
-
70350247861
-
Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques
-
Zhao, Y., and Jensen, O. N. (2009) Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics 9, 4632-4641
-
(2009)
Proteomics
, vol.9
, pp. 4632-4641
-
-
Zhao, Y.1
Jensen, O.N.2
-
11
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
DOI 10.1038/nmeth1019, PII NMETH1019
-
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 (Pubitemid 46358868)
-
(2007)
Nature Methods
, vol.4
, Issue.3
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
12
-
-
79953212975
-
Confident phosphorylation site localization using the Mascot Delta Score
-
Savitski, M. M., Lemeer, S., Boesche, M., Lang, M., Mathieson, T., Bantscheff, M., and Kuster, B. (2011) Confident phosphorylation site localization using the Mascot Delta Score. Mol. Cell Proteomics
-
(2011)
Mol. Cell Proteomics
-
-
Savitski, M.M.1
Lemeer, S.2
Boesche, M.3
Lang, M.4
Mathieson, T.5
Bantscheff, M.6
Kuster, B.7
-
13
-
-
79960181605
-
Modification site localization scoring integrated into a search engine
-
M111.008078
-
Baker, P. R., Trinidad, J. C., and Chalkley, R. J. (2011) Modification site localization scoring integrated into a search engine. Mol. Cell Proteomics M111.008078
-
(2011)
Mol. Cell Proteomics
-
-
Baker, P.R.1
Trinidad, J.C.2
Chalkley, R.J.3
-
14
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
15
-
-
47849125967
-
A multidimensional chromatography technology for in-depth phosphoproteome analysis
-
DOI 10.1074/mcp.M700468-MCP200
-
Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., and Zhou, H. (2008) A multidimensional chromatography technology for indepth phosphoproteome analysis. Mol. Cell Proteomics 7, 1389-1396 (Pubitemid 352038280)
-
(2008)
Molecular and Cellular Proteomics
, vol.7
, Issue.7
, pp. 1389-1396
-
-
Albuquerque, C.P.1
Smolka, M.B.2
Payne, S.H.3
Bafna, V.4
Eng, J.5
Zhou, H.6
-
16
-
-
84872052101
-
-
Available from
-
Spectrum Mill - Agilent Technologies Inc.; Available from: http://www.chem.agilent.com/en-US/Products/software/chromatography/ms/ spectrummillformasshunterworkstation/pages/default.aspx
-
Spectrum Mill
-
-
-
17
-
-
33749853607
-
A probability-based approach for high-throughput protein phosphorylation analysis and site localization
-
DOI 10.1038/nbt1240, PII NBT1240
-
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 24, 1285-1292 (Pubitemid 44564776)
-
(2006)
Nature Biotechnology
, vol.24
, Issue.10
, pp. 1285-1292
-
-
Beausoleil, S.A.1
Villen, J.2
Gerber, S.A.3
Rush, J.4
Gygi, S.P.5
-
18
-
-
33750456519
-
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
-
DOI 10.1016/j.cell.2006.09.026, PII S0092867406012748
-
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., and Mann, M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648 (Pubitemid 44647421)
-
(2006)
Cell
, vol.127
, Issue.3
, pp. 635-648
-
-
Olsen, J.V.1
Blagoev, B.2
Gnad, F.3
Macek, B.4
Kumar, C.5
Mortensen, P.6
Mann, M.7
-
19
-
-
51649090664
-
PhosphoScore: An open-source phosphorylation site assignment tool for MSn data
-
Ruttenberg, B. E., Pisitkun, T., Knepper, M. A., and Hoffert, J. D. (2008) PhosphoScore: an open-source phosphorylation site assignment tool for MSn data. J. Proteome Res. 7, 3054-3059
-
(2008)
J. Proteome Res.
, vol.7
, pp. 3054-3059
-
-
Ruttenberg, B.E.1
Pisitkun, T.2
Knepper, M.A.3
Hoffert, J.D.4
-
20
-
-
65249185673
-
SLoMo: Automated site localization of modifications from ETD/ECD mass spectra
-
Bailey, C. M., Sweet, S. M., Cunningham, D. L., Zeller, M., Heath, J. K., and Cooper, H. J. (2009) SLoMo: automated site localization of modifications from ETD/ECD mass spectra. J. Proteome Res. 8, 1965-1971
-
(2009)
J. Proteome Res.
, vol.8
, pp. 1965-1971
-
-
Bailey, C.M.1
Sweet, S.M.2
Cunningham, D.L.3
Zeller, M.4
Heath, J.K.5
Cooper, H.J.6
-
21
-
-
59049086847
-
Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry
-
Swaney, D. L., Wenger, C. D., Thomson, J. A., and Coon, J. J. (2009) Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 106, 995-1000
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 995-1000
-
-
Swaney, D.L.1
Wenger, C.D.2
Thomson, J.A.3
Coon, J.J.4
-
22
-
-
82755182013
-
Universal and confident phosphorylation site localization using phosphoRS
-
Taus, T., Kocher, T., Pichler, P., Paschke, C., Schmidt, A., Henrich, C., and Mechtler, K. (2011) Universal and confident phosphorylation site localization using phosphoRS. J. Proteome Res. 10, 5354-5362
-
(2011)
J. Proteome Res.
, vol.10
, pp. 5354-5362
-
-
Taus, T.1
Kocher, T.2
Pichler, P.3
Paschke, C.4
Schmidt, A.5
Henrich, C.6
Mechtler, K.7
-
23
-
-
70349574233
-
An unsupervised, model-free, machine-learning combiner for peptide identifications from tandem mass spectra
-
Edwards, N., Wu, X., and Tseng, C. W. (2009) An unsupervised, model-free, machine-learning combiner for peptide identifications from tandem mass spectra. Clin. Proteomics 5, 23-36
-
(2009)
Clin. Proteomics
, vol.5
, pp. 23-36
-
-
Edwards, N.1
Wu, X.2
Tseng, C.W.3
-
24
-
-
33646907086
-
Reporting protein identification data: The next generation of guidelines
-
DOI 10.1074/mcp.E600005-MCP200
-
Bradshaw, R. A., Burlingame, A. L., Carr, S., and Aebersold, R. (2006) Reporting protein identification data: the next generation of guidelines. Mol. Cell Proteomics 5, 787-788 (Pubitemid 43792788)
-
(2006)
Molecular and Cellular Proteomics
, vol.5
, Issue.5
, pp. 787-788
-
-
Bradshaw, R.A.1
Burlingame, A.L.2
Carr, S.3
Aebersold, R.4
-
25
-
-
84872052765
-
-
Available from
-
Rudnick, P. A., Askenazi, M., Clauser, K. R., Lane, W. S., Martens, L., McDonald, W. H., Mertins, P., Meyer-Arendt, K., Searle, B. C., and Kowalak, J. A. Proteome Informatics Research Group 2010 Study. Available from: http://www.abrf.org/index.cfm/group.show/ProteomicsInformaticsResearchGroup.53. htm
-
Proteome Informatics Research Group 2010 Study
-
-
Rudnick, P.A.1
Askenazi, M.2
Clauser, K.R.3
Lane, W.S.4
Martens, L.5
McDonald, W.H.6
Mertins, P.7
Meyer-Arendt, K.8
Searle, B.C.9
Kowalak, J.A.10
-
26
-
-
80053374337
-
Proteomic and phosphoproteomic comparison of human ES and iPS cells
-
Phanstiel, D. H., Brumbaugh, J., Wenger, C. D., Tian, S., Probasco, M. D., Bailey, D. J., Swaney, D. L., Tervo, M. A., Bolin, J. M., Ruotti, V., Stewart, R., Thomson, J. A., and Coon, J. J. (2011) Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat. Methods 8, 821-827
-
(2011)
Nat. Methods
, vol.8
, pp. 821-827
-
-
Phanstiel, D.H.1
Brumbaugh, J.2
Wenger, C.D.3
Tian, S.4
Probasco, M.D.5
Bailey, D.J.6
Swaney, D.L.7
Tervo, M.A.8
Bolin, J.M.9
Ruotti, V.10
Stewart, R.11
Thomson, J.A.12
Coon, J.J.13
-
27
-
-
84872053257
-
-
Available from
-
PepArML. Available from: https://edwardslab.bmcb.georgetown.edu/pymsio/.
-
PepArML
-
-
-
28
-
-
78650466243
-
A tissue-specific atlas of mouse protein phosphorylation and expression
-
Huttlin, E. L., Jedrychowski, M. P., Elias, J. E., Goswami, T., Rad, R., Beausoleil, S. A., Villén, J., Haas, W., Sowa, M. E., and Gygi, S. P. (2010) A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174-1189
-
(2010)
Cell
, vol.143
, pp. 1174-1189
-
-
Huttlin, E.L.1
Jedrychowski, M.P.2
Elias, J.E.3
Goswami, T.4
Rad, R.5
Beausoleil, S.A.6
Villén, J.7
Haas, W.8
Sowa, M.E.9
Gygi, S.P.10
-
29
-
-
77957221582
-
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
-
Nesvizhskii, A. I. (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 73, 2092-2123
-
(2010)
J. Proteomics
, vol.73
, pp. 2092-2123
-
-
Nesvizhskii, A.I.1
-
30
-
-
79952197054
-
Tandem mass spectrometry spectral libraries and library searching
-
Deutsch, E. W. (2011) Tandem mass spectrometry spectral libraries and library searching. Methods Mol. Biol. 696, 225-232
-
(2011)
Methods Mol. Biol.
, vol.696
, pp. 225-232
-
-
Deutsch, E.W.1
-
31
-
-
84857047339
-
PhosphoSitePlus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
-
Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V., and Sullivan, M. (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.DATABASE ISSUE
-
-
Hornbeck, P.V.1
Kornhauser, J.M.2
Tkachev, S.3
Zhang, B.4
Skrzypek, E.5
Murray, B.6
Latham, V.7
Sullivan, M.8
-
32
-
-
78651320816
-
Phospho.ELM: A database of phosphorylation sites-update 2011
-
Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, L. J., Gibson, T. J., and Diella, F. (2011) Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res. 39(Database issue), D261-7
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.DATABASE ISSUE
-
-
Dinkel, H.1
Chica, C.2
Via, A.3
Gould, C.M.4
Jensen, L.J.5
Gibson, T.J.6
Diella, F.7
-
33
-
-
78651277460
-
PHOSIDA 2011: The posttranslational modification database
-
Gnad, F., Gunawardena, J., and Mann, M. (2011) PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 39(Data-base issue), D253-60
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.DATABASE ISSUE
-
-
Gnad, F.1
Gunawardena, J.2
Mann, M.3
-
34
-
-
67049158217
-
Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides
-
Chalkley, R. J., Thalhammer, A., Schoepfer, R., and Burlingame, A. L. (2009) Identification of protein O-GlcNAcylation sites using electron transfer dissociation mass spectrometry on native peptides. Proc. Natl. Acad. Sci. U.S.A. 106, 8894-8899
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 8894-8899
-
-
Chalkley, R.J.1
Thalhammer, A.2
Schoepfer, R.3
Burlingame, A.L.4
-
35
-
-
79952197632
-
MzIdentML: An open community-built standard format for the results of proteomics spectrum identification algorithms
-
Eisenacher, M. (2011) mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms. Methods Mol Biol. 696, 161-177
-
(2011)
Methods Mol Biol.
, vol.696
, pp. 161-177
-
-
Eisenacher, M.1
|