-
1
-
-
84890367496
-
Mass spectrometry-driven phosphoproteomics: Patterning the systems biology mosaic
-
Jünger, M. A.; Aebersold, R. Mass spectrometry-driven phosphoproteomics: Patterning the systems biology mosaic Dev. Biol. 2014, 3, 83-112
-
(2014)
Dev. Biol.
, vol.3
, pp. 83-112
-
-
Jünger, M.A.1
Aebersold, R.2
-
2
-
-
63049113651
-
Analytical strategies for phosphoproteomics
-
Thingholm, T. E.; Jensen, O. N.; Larsen, M. R. Analytical strategies for phosphoproteomics Proteomics 2009, 9 (6) 1451-68
-
(2009)
Proteomics
, vol.9
, Issue.6
, pp. 1451-1468
-
-
Thingholm, T.E.1
Jensen, O.N.2
Larsen, M.R.3
-
3
-
-
81055140468
-
Phosphoproteomics: Searching for a needle in a haystack
-
Tichy, A.; Salovska, B.; Rehulka, P.; Klimentova, J.; Vavrova, J.; Stulik, J.; Hernychova, L. Phosphoproteomics: Searching for a needle in a haystack J. Proteomics 2011, 74 (12) 2786-97
-
(2011)
J. Proteomics
, vol.74
, Issue.12
, pp. 2786-2797
-
-
Tichy, A.1
Salovska, B.2
Rehulka, P.3
Klimentova, J.4
Vavrova, J.5
Stulik, J.6
Hernychova, L.7
-
4
-
-
84890641204
-
The coming of age of phosphoproteomics-From large data sets to inference of protein functions
-
Roux, P. P.; Thibault, P. The coming of age of phosphoproteomics-From large data sets to inference of protein functions Mol. Cell. Proteomics 2013, 12 (12) 3453-64
-
(2013)
Mol. Cell. Proteomics
, vol.12
, Issue.12
, pp. 3453-3464
-
-
Roux, P.P.1
Thibault, P.2
-
5
-
-
84874589189
-
Mapping and analysis of phosphorylation sites: A quick guide for cell biologists
-
Dephoure, N.; Gould, K. L.; Gygi, S. P.; Kellogg, D. R. Mapping and analysis of phosphorylation sites: A quick guide for cell biologists Mol. Biol. Cell 2013, 24 (5) 535-42
-
(2013)
Mol. Biol. Cell
, vol.24
, Issue.5
, pp. 535-542
-
-
Dephoure, N.1
Gould, K.L.2
Gygi, S.P.3
Kellogg, D.R.4
-
6
-
-
84855932755
-
Advances in quantitative phosphoproteomics
-
Nilsson, C. L. Advances in quantitative phosphoproteomics Anal. Chem. 2012, 84 (2) 735-46
-
(2012)
Anal. Chem.
, vol.84
, Issue.2
, pp. 735-746
-
-
Nilsson, C.L.1
-
7
-
-
84879344463
-
Optimized fragmentation conditions for iTRAQ-labeled phosphopeptides
-
Linke, D.; Hung, C. W.; Cassidy, L.; Tholey, A. Optimized fragmentation conditions for iTRAQ-labeled phosphopeptides J. Proteome Res. 2013, 12 (6) 2755-63
-
(2013)
J. Proteome Res.
, vol.12
, Issue.6
, pp. 2755-2763
-
-
Linke, D.1
Hung, C.W.2
Cassidy, L.3
Tholey, A.4
-
8
-
-
77951644400
-
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
-
Olsen, J. V.; Vermeulen, M.; Santamaria, A.; Kumar, C.; Miller, M. L.; Jensen, L. J.; Gnad, F.; Cox, J.; Jensen, T. S.; Nigg, E. A.; Brunak, S.; Mann, M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis Sci. Signaling 2010, 3 (104) ra3
-
(2010)
Sci. Signaling
, vol.3
, Issue.104
, pp. 3
-
-
Olsen, J.V.1
Vermeulen, M.2
Santamaria, A.3
Kumar, C.4
Miller, M.L.5
Jensen, L.J.6
Gnad, F.7
Cox, J.8
Jensen, T.S.9
Nigg, E.A.10
Brunak, S.11
Mann, M.12
-
9
-
-
80053342612
-
A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast
-
Harvey, S. L.; Enciso, G.; Dephoure, N.; Gygi, S. P.; Gunawardena, J.; Kellogg, D. R. A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast Mol. Biol. Cell 2011, 22 (19) 3595-608
-
(2011)
Mol. Biol. Cell
, vol.22
, Issue.19
, pp. 3595-3608
-
-
Harvey, S.L.1
Enciso, G.2
Dephoure, N.3
Gygi, S.P.4
Gunawardena, J.5
Kellogg, D.R.6
-
10
-
-
77149162668
-
Peptide and protein quantification: A map of the minefield
-
Vaudel, M.; Sickmann, A.; Martens, L. Peptide and protein quantification: A map of the minefield Proteomics 2010, 10 (4) 650-70
-
(2010)
Proteomics
, vol.10
, Issue.4
, pp. 650-670
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
11
-
-
0036914002
-
N-Terminal peptide labeling strategy for incorporation of isotopic tags: A method for the determination of site-specific absolute phosphorylation stoichiometry
-
Zhang, X.; Jin, Q. K.; Carr, S. A.; Annan, R. S. N-Terminal peptide labeling strategy for incorporation of isotopic tags: A method for the determination of site-specific absolute phosphorylation stoichiometry Rapid Commun. Mass Spectrom. 2002, 16 (24) 2325-32
-
(2002)
Rapid Commun. Mass Spectrom.
, vol.16
, Issue.24
, pp. 2325-2332
-
-
Zhang, X.1
Jin, Q.K.2
Carr, S.A.3
Annan, R.S.4
-
12
-
-
39749146978
-
Quantitative proteomic analysis of protein complexes: Concurrent identification of interactors and their state of phosphorylation
-
Pflieger, D.; Junger, M. A.; Muller, M.; Rinner, O.; Lee, H.; Gehrig, P. M.; Gstaiger, M.; Aebersold, R. Quantitative proteomic analysis of protein complexes: Concurrent identification of interactors and their state of phosphorylation Mol. Cell. Proteomics 2008, 7 (2) 326-46
-
(2008)
Mol. Cell. Proteomics
, vol.7
, Issue.2
, pp. 326-346
-
-
Pflieger, D.1
Junger, M.A.2
Muller, M.3
Rinner, O.4
Lee, H.5
Gehrig, P.M.6
Gstaiger, M.7
Aebersold, R.8
-
13
-
-
0037417791
-
Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry
-
Bonenfant, D.; Schmelzle, T.; Jacinto, E.; Crespo, J. L.; Mini, T.; Hall, M. N.; Jenoe, P. Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry Proc. Natl. Acad. Sci. U. S. A. 2003, 100 (3) 880-5
-
(2003)
Proc. Natl. Acad. Sci. U. S. A.
, vol.100
, Issue.3
, pp. 880-885
-
-
Bonenfant, D.1
Schmelzle, T.2
Jacinto, E.3
Crespo, J.L.4
Mini, T.5
Hall, M.N.6
Jenoe, P.7
-
14
-
-
77954185457
-
Assay development for the determination of phosphorylation stoichiometry using multiple reaction monitoring methods with and without phosphatase treatment: Application to breast cancer signaling pathways
-
Domanski, D.; Murphy, L. C.; Borchers, C. H. Assay development for the determination of phosphorylation stoichiometry using multiple reaction monitoring methods with and without phosphatase treatment: Application to breast cancer signaling pathways Anal. Chem. 2010, 82 (13) 5610-20
-
(2010)
Anal. Chem.
, vol.82
, Issue.13
, pp. 5610-5620
-
-
Domanski, D.1
Murphy, L.C.2
Borchers, C.H.3
-
15
-
-
2342583505
-
An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins
-
Hegeman, A. D.; Harms, A. C.; Sussman, M. R.; Bunner, A. E.; Harper, J. F. An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins J. Am. Soc. Mass Spectrom. 2004, 15 (5) 647-53
-
(2004)
J. Am. Soc. Mass Spectrom.
, vol.15
, Issue.5
, pp. 647-653
-
-
Hegeman, A.D.1
Harms, A.C.2
Sussman, M.R.3
Bunner, A.E.4
Harper, J.F.5
-
16
-
-
70449498714
-
Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry
-
Johnson, H.; Eyers, C. E.; Eyers, P. A.; Beynon, R. J.; Gaskell, S. J. Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry J. Am. Soc. Mass Spectrom. 2009, 20 (12) 2211-20
-
(2009)
J. Am. Soc. Mass Spectrom.
, vol.20
, Issue.12
, pp. 2211-2220
-
-
Johnson, H.1
Eyers, C.E.2
Eyers, P.A.3
Beynon, R.J.4
Gaskell, S.J.5
-
17
-
-
70949092257
-
The stoichiometry of protein phosphorylation in adipocyte lipid droplets: Analysis by N-terminal isotope tagging and enzymatic dephosphorylation
-
Kanshin, E.; Wang, S.; Ashmarina, L.; Fedjaev, M.; Nifant'ev, I.; Mitchell, G. A.; Pshezhetsky, A. V. The stoichiometry of protein phosphorylation in adipocyte lipid droplets: Analysis by N-terminal isotope tagging and enzymatic dephosphorylation Proteomics 2009, 9 (22) 5067-77
-
(2009)
Proteomics
, vol.9
, Issue.22
, pp. 5067-5077
-
-
Kanshin, E.1
Wang, S.2
Ashmarina, L.3
Fedjaev, M.4
Nifant'Ev, I.5
Mitchell, G.A.6
Pshezhetsky, A.V.7
-
18
-
-
49449114411
-
Quantification of protein phosphorylation by liquid chromatography-mass spectrometry
-
Previs, M. J.; VanBuren, P.; Begin, K. J.; Vigoreaux, J. O.; LeWinter, M. M.; Matthews, D. E. Quantification of protein phosphorylation by liquid chromatography-mass spectrometry Anal. Chem. 2008, 80 (15) 5864-72
-
(2008)
Anal. Chem.
, vol.80
, Issue.15
, pp. 5864-5872
-
-
Previs, M.J.1
Vanburen, P.2
Begin, K.J.3
Vigoreaux, J.O.4
Lewinter, M.M.5
Matthews, D.E.6
-
19
-
-
77957326091
-
Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument
-
Przybylski, C.; Junger, M. A.; Aubertin, J.; Radvanyi, F.; Aebersold, R.; Pflieger, D. Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument J. Proteome Res. 2010, 9 (10) 5118-32
-
(2010)
J. Proteome Res.
, vol.9
, Issue.10
, pp. 5118-5132
-
-
Przybylski, C.1
Junger, M.A.2
Aubertin, J.3
Radvanyi, F.4
Aebersold, R.5
Pflieger, D.6
-
20
-
-
79960979428
-
A large-scale method to measure absolute protein phosphorylation stoichiometries
-
Wu, R.; Haas, W.; Dephoure, N.; Huttlin, E. L.; Zhai, B.; Sowa, M. E.; Gygi, S. P. A large-scale method to measure absolute protein phosphorylation stoichiometries Nat. Methods 2011, 8 (8) 677-83
-
(2011)
Nat. Methods
, vol.8
, Issue.8
, pp. 677-683
-
-
Wu, R.1
Haas, W.2
Dephoure, N.3
Huttlin, E.L.4
Zhai, B.5
Sowa, M.E.6
Gygi, S.P.7
-
21
-
-
84887056777
-
Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation
-
Hebert, A. S.; Merrill, A. E.; Stefely, J. A.; Bailey, D. J.; Wenger, C. D.; Westphall, M. S.; Pagliarini, D. J.; Coon, J. J. Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation Mol. Cell. Proteomics 2013, 12 (11) 3360-9
-
(2013)
Mol. Cell. Proteomics
, vol.12
, Issue.11
, pp. 3360-3369
-
-
Hebert, A.S.1
Merrill, A.E.2
Stefely, J.A.3
Bailey, D.J.4
Wenger, C.D.5
Westphall, M.S.6
Pagliarini, D.J.7
Coon, J.J.8
-
22
-
-
84857886553
-
Novel mass spectrometric method for phosphorylation quantification using cerium oxide nanoparticles and tandem mass tags
-
Jia, W.; Andaya, A.; Leary, J. A. Novel mass spectrometric method for phosphorylation quantification using cerium oxide nanoparticles and tandem mass tags Anal. Chem. 2012, 84 (5) 2466-73
-
(2012)
Anal. Chem.
, vol.84
, Issue.5
, pp. 2466-2473
-
-
Jia, W.1
Andaya, A.2
Leary, J.A.3
-
23
-
-
33750456519
-
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
-
Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 2006, 127 (3) 635-48
-
(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
-
24
-
-
84895748316
-
ITRAQ as a method for optimization: Enhancing peptide recovery after gel fractionation
-
Glibert, P.; Van Steendam, K.; Dhaenens, M.; Deforce, D. iTRAQ as a method for optimization: Enhancing peptide recovery after gel fractionation Proteomics 2014, 14 (6) 680-4
-
(2014)
Proteomics
, vol.14
, Issue.6
, pp. 680-684
-
-
Glibert, P.1
Van Steendam, K.2
Dhaenens, M.3
Deforce, D.4
-
25
-
-
0036807449
-
Error-tolerant searching of uninterpreted tandem mass spectrometry data
-
Creasy, D. M.; Cottrell, J. S. Error-tolerant searching of uninterpreted tandem mass spectrometry data Proteomics 2002, 2 (10) 1426-34
-
(2002)
Proteomics
, vol.2
, Issue.10
, pp. 1426-1434
-
-
Creasy, D.M.1
Cottrell, J.S.2
-
26
-
-
77949681441
-
Rover: A tool to visualize and validate quantitative proteomics data from different sources
-
Colaert, N.; Helsens, K.; Impens, F.; Vandekerckhove, J.; Gevaert, K. Rover: A tool to visualize and validate quantitative proteomics data from different sources Proteomics 2010, 10 (6) 1226-9
-
(2010)
Proteomics
, vol.10
, Issue.6
, pp. 1226-1229
-
-
Colaert, N.1
Helsens, K.2
Impens, F.3
Vandekerckhove, J.4
Gevaert, K.5
-
27
-
-
84874762979
-
The proteomics identifications (PRIDE) database and associated tools: Status in 2013
-
Vizcaino, J. A.; Cote, R. G.; Csordas, A.; Dianes, J. A.; Fabregat, A.; Foster, J. M.; Griss, J.; Alpi, E.; Birim, M.; Contell, J.; O'Kelly, G.; Schoenegger, A.; Ovelleiro, D.; Perez-Riverol, Y.; Reisinger, F.; Rios, D.; Wang, R.; Hermjakob, H. The proteomics identifications (PRIDE) database and associated tools: Status in 2013 Nucleic Acids Res. 2013, 41 (Database issue) D1063-9
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.DATABASE ISSUE
, pp. 1063-1069
-
-
Vizcaino, J.A.1
Cote, R.G.2
Csordas, A.3
Dianes, J.A.4
Fabregat, A.5
Foster, J.M.6
Griss, J.7
Alpi, E.8
Birim, M.9
Contell, J.10
O'Kelly, G.11
Schoenegger, A.12
Ovelleiro, D.13
Perez-Riverol, Y.14
Reisinger, F.15
Rios, D.16
Wang, R.17
Hermjakob, H.18
-
28
-
-
84890644637
-
Status of large-scale analysis of post-translational modifications by mass spectrometry
-
Olsen, J. V.; Mann, M. Status of large-scale analysis of post-translational modifications by mass spectrometry Mol. Cell. Proteomics 2013, 12 (12) 3444-52
-
(2013)
Mol. Cell. Proteomics
, vol.12
, Issue.12
, pp. 3444-3452
-
-
Olsen, J.V.1
Mann, M.2
-
29
-
-
70449412362
-
ITRAQ underestimation in simple and complex mixtures: The good, the bad, and the ugly
-
Ow, S. Y.; Salim, M.; Noirel, J.; Evans, C.; Rehman, I.; Wright, P. C. iTRAQ underestimation in simple and complex mixtures: The good, the bad, and the ugly J. Proteome Res. 2009, 8 (11) 5347-55
-
(2009)
J. Proteome Res.
, vol.8
, Issue.11
, pp. 5347-5355
-
-
Ow, S.Y.1
Salim, M.2
Noirel, J.3
Evans, C.4
Rehman, I.5
Wright, P.C.6
-
30
-
-
84865603658
-
An insight into iTRAQ: Where do we stand now?
-
Evans, C.; Noirel, J.; Ow, S. Y.; Salim, M.; Pereira-Medrano, A. G.; Couto, N.; Pandhal, J.; Smith, D.; Pham, T. K.; Karunakaran, E.; Zou, X.; Biggs, C. A.; Wright, P. C. An insight into iTRAQ: Where do we stand now? Anal. Bioanal. Chem. 2012, 404 (4) 1011-27
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, Issue.4
, pp. 1011-1027
-
-
Evans, C.1
Noirel, J.2
Ow, S.Y.3
Salim, M.4
Pereira-Medrano, A.G.5
Couto, N.6
Pandhal, J.7
Smith, D.8
Pham, T.K.9
Karunakaran, E.10
Zou, X.11
Biggs, C.A.12
Wright, P.C.13
-
31
-
-
80155150331
-
Taming the isobaric tagging elephant in the room in quantitative proteomics
-
Christoforou, A.; Lilley, K. S. Taming the isobaric tagging elephant in the room in quantitative proteomics Nat. Methods 2011, 8 (11) 911-3
-
(2011)
Nat. Methods
, vol.8
, Issue.11
, pp. 911-913
-
-
Christoforou, A.1
Lilley, K.S.2
-
32
-
-
84867443197
-
Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)
-
Vaudel, M.; Burkhart, J. M.; Radau, S.; Zahedi, R. P.; Martens, L.; Sickmann, A. Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI) J. Proteome Res. 2012, 11 (10) 5072-80
-
(2012)
J. Proteome Res.
, vol.11
, Issue.10
, pp. 5072-5080
-
-
Vaudel, M.1
Burkhart, J.M.2
Radau, S.3
Zahedi, R.P.4
Martens, L.5
Sickmann, A.6
-
33
-
-
80155124832
-
MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
-
Ting, L.; Rad, R.; Gygi, S. P.; Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics Nat. Methods 2011, 8 (11) 937-40
-
(2011)
Nat. Methods
, vol.8
, Issue.11
, pp. 937-940
-
-
Ting, L.1
Rad, R.2
Gygi, S.P.3
Haas, W.4
-
34
-
-
84897041394
-
Improved isobaric tandem mass tag quantification by ion mobility mass spectrometry
-
Sturm, R. M.; Lietz, C. B.; Li, L. Improved isobaric tandem mass tag quantification by ion mobility mass spectrometry Rapid Commun. Mass Spectrom. 2014, 28 (9) 1051-60
-
(2014)
Rapid Commun. Mass Spectrom.
, vol.28
, Issue.9
, pp. 1051-1060
-
-
Sturm, R.M.1
Lietz, C.B.2
Li, L.3
-
35
-
-
84922325341
-
Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification
-
Christoforou, A.; Arias, A. M.; Lilley, K. S. Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification Methods Mol. Biol. 2014, 1156, 157-74
-
(2014)
Methods Mol. Biol.
, vol.1156
, pp. 157-174
-
-
Christoforou, A.1
Arias, A.M.2
Lilley, K.S.3
-
36
-
-
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.; Sullivan, M. PhosphoSitePlus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse Nucleic Acids Res. 2012, 40 (Database issue) D261-70
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.DATABASE ISSUE
, pp. 261-270
-
-
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
-
37
-
-
84865576726
-
Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present
-
Bantscheff, M.; Lemeer, S.; Savitski, M. M.; Kuster, B. Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present Anal. Bioanal. Chem. 2012, 404 (4) 939-65
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, Issue.4
, pp. 939-965
-
-
Bantscheff, M.1
Lemeer, S.2
Savitski, M.M.3
Kuster, B.4
-
38
-
-
79960976768
-
UniProt knowledgebase: A hub of integrated protein data
-
Magrane, M.; Consortium, U. UniProt knowledgebase: A hub of integrated protein data Database (Oxford) 2011, 2011, bar009
-
(2011)
Database (Oxford)
, vol.2011
, pp. 009
-
-
Magrane, M.1
Consortium, U.2
-
39
-
-
84874998505
-
D-score: A search engine independent MD-score
-
Vaudel, M.; Breiter, D.; Beck, F.; Rahnenfuhrer, J.; Martens, L.; Zahedi, R. P. D-score: A search engine independent MD-score Proteomics 2013, 13 (6) 1036-41
-
(2013)
Proteomics
, vol.13
, Issue.6
, pp. 1036-1041
-
-
Vaudel, M.1
Breiter, D.2
Beck, F.3
Rahnenfuhrer, J.4
Martens, L.5
Zahedi, R.P.6
-
40
-
-
77958000048
-
Comparative assessment of site assignments in CID and electron transfer dissociation spectra of phosphopeptides discloses limited relocation of phosphate groups
-
Mischerikow, N.; Altelaar, A. F.; Navarro, J. D.; Mohammed, S.; Heck, A. J. Comparative assessment of site assignments in CID and electron transfer dissociation spectra of phosphopeptides discloses limited relocation of phosphate groups Mol. Cell. Proteomics 2010, 9 (10) 2140-8
-
(2010)
Mol. Cell. Proteomics
, vol.9
, Issue.10
, pp. 2140-2148
-
-
Mischerikow, N.1
Altelaar, A.F.2
Navarro, J.D.3
Mohammed, S.4
Heck, A.J.5
|