Decoding signalling networks by mass spectrometry-based proteomics.
Signalling networks regulate essentially all of the biology of cells and organisms in normal and disease states. Signalling is often studied using antibody-based techniques such as western blots. Large-scale 'precision proteomics' based on mass spectrometry now enables the system-wide characterization of signalling events at the levels of post-translational modifications, protein-protein interactions and changes in protein expression. This technology delivers accurate and unbiased information about the quantitative changes of thousands of proteins and their modifications in response to any perturbation. Current studies focus on phosphorylation, but acetylation, methylation, glycosylation and ubiquitylation are also becoming amenable to investigation. Large-scale proteomics-based signalling research will fundamentally change our understanding of signalling networks.
Choudhary
Chunaram
C
The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. chuna.choudhary@cpr.ku.dk
Mann
Matthias
M
D000818:Animals; D006801:Humans; D013058:Mass Spectrometry; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D015398:Signal Transduction
D020543:Proteome
Cell Stem Cell. 2009 Aug 7;5(2):214-26
19664995
Science. 2005 Jun 3;308(5727):1472-7
15933201
Nat Biotechnol. 2006 Oct;24(10):1285-92
16964243
Science. 2009 Dec 11;326(5959):1502-9
20007894
Science. 2006 Mar 3;311(5765):1293-7
16513984
FEBS Lett. 2009 Jun 5;583(11):1703-12
19306877
Genes Dev. 2009 Aug 15;23(16):1929-43
19684113
Cell Host Microbe. 2009 Apr 23;5(4):397-403
19380118
Nat Methods. 2004 Nov;1(2):119-26
15782174
Cell. 2008 Jul 25;134(2):353-64
18662549
J Proteome Res. 2008 Sep;7(9):3900-10
18698806
Nature. 2003 Oct 16;425(6959):686-91
14562095
Genome Biol. 2007;8(11):R250
18039369
Nat Methods. 2007 Oct;4(10):798-806
17901869
Proteomics. 2008 Nov;8(21):4534-46
18846507
Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19855-60
18077418
Anal Chem. 2000 Feb 1;72(3):563-73
10695143
Nat Biotechnol. 2007 May;25(5):576-83
17450130
Sci Signal. 2009 May 26;2(72):ra24
19471022
Mol Syst Biol. 2005;1:2005.0008
16729043
Sci Signal. 2010 Jan 12;3(104):ra3
20068231
Nat Methods. 2009 Oct;6(10):741-4
19749761
Methods Mol Biol. 2010;604:55-71
20013364
Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711
15340378
Science. 2007 May 25;316(5828):1160-6
17525332
Science. 2009 Sep 25;325(5948):1682-6
19779198
Anal Chem. 1992 Jun 15;64(12):467R-502R
1626707
Mol Biosyst. 2009 Oct;5(10):1112-21
19756300
Cell. 2007 Dec 14;131(6):1190-203
18083107
Methods Mol Biol. 2010;604:273-83
20013377
Anal Chem. 2006 Apr 1;78(7):2113-20
16579588
Proteomics. 2009 Oct;9(20):4632-41
19743430
Nat Methods. 2006 Jul;3(7):533-9
16791211
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18132-8
18818311
Cell. 2009 Aug 21;138(4):795-806
19664813
Nat Cell Biol. 2009 Dec;11(12):1458-64
19935650
Mol Cell. 2008 Aug 8;31(3):438-48
18691976
Nat Methods. 2010 May;7(5):383-5
20364148
Sci Signal. 2009 Jul 28;2(81):ra39
19638616
Nature. 2008 Oct 30;455(7217):1251-4
18820680
Mol Cell Proteomics. 2008 Sep;7(9):1763-77
18515860
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10364-9
17563356
Immunity. 2010 Feb 26;32(2):279-89
20171123
Anal Chem. 2004 Jul 1;76(13):3590-8
15228329
Nature. 2003 Oct 16;425(6959):737-41
14562106
Nat Protoc. 2009;4(4):484-94
19300442
Curr Opin Chem Biol. 2009 Dec;13(5-6):510-7
19775930
Nat Methods. 2007 Sep;4(9):709-12
17721543
Nat Rev Mol Cell Biol. 2006 Dec;7(12):952-8
17139335
Proteomics. 2008 Nov;8(21):4433-43
18846511
Nature. 2001 May 17;411(6835):355-65
11357143
Mol Cell Proteomics. 2009 Jan;8(1):157-71
18782753
Nat Genet. 2000 May;25(1):25-9
10802651
Mol Cell Proteomics. 2008 Jan;7(1):132-44
17938407
Mol Cell Proteomics. 2009 Aug;8(8):1908-20
19429919
Nat Rev Mol Cell Biol. 2006 Jun;7(6):391-403
16723975
J Proteome Res. 2009 Oct;8(10):4553-63
19691289
Nat Biotechnol. 2008 Dec;26(12):1367-72
19029910
Nat Biotechnol. 2003 Mar;21(3):315-8
12577067
Science. 2009 Aug 14;325(5942):834-40
19608861
Mol Biosyst. 2009 Nov;5(11):1337-46
19823750
Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6069-74
18420821
Mol Cell Proteomics. 2009 Dec;8(12):2759-69
19828875
Annu Rev Pharmacol Toxicol. 2009;49:199-221
18834307
Mol Cell Proteomics. 2010 May;9(5):780-90
20019052
Nat Biotechnol. 2001 Mar;19(3):242-7
11231557
Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5860-5
17389395
Science. 2006 Apr 14;312(5771):212-7
16614208
Mol Cell Proteomics. 2009 Dec;8(12):2796-808
19651622
Mol Cell Proteomics. 2005 Mar;4(3):310-27
15665377
Nat Biotechnol. 2007 Jan;25(1):125-31
17195840
Nat Biotechnol. 2003 Aug;21(8):921-6
12872131
Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):995-1000
19144917
Cell Stem Cell. 2009 Aug 7;5(2):204-13
19664994
J Proteome Res. 2004 May-Jun;3(3):621-6
15253445
Mol Cell Proteomics. 2007 Aug;6(8):1416-27
17510050
Nat Biotechnol. 2008 Jan;26(1):127-32
18183025
Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
17593931
Mol Cell Proteomics. 2005 Dec;4(12):2010-21
16249172
Mol Cell Proteomics. 2009 May;8(5):959-70
19151416
Nat Protoc. 2009;4(6):870-7
19444244
Nat Rev Mol Cell Biol. 2006 Jul;7(7):473-83
16829979
Mol Cell Proteomics. 2004 Dec;3(12):1154-69
15385600
Science. 2007 Nov 30;318(5855):1402-7
18048679
Anal Chem. 2003 Dec 15;75(24):6843-52
14670044
Curr Opin Biotechnol. 2008 Aug;19(4):331-7
18590817
Mol Cell. 2006 Aug;23(4):607-18
16916647
Immunity. 2009 Jan 16;30(1):143-54
19144319
Nat Biotechnol. 1999 Jul;17(7):676-82
10404161
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2451-6
18268350
Nat Biotechnol. 2007 Sep;25(9):1035-44
17721511
Mol Cell Proteomics. 2002 May;1(5):376-86
12118079
Cell. 2006 Nov 3;127(3):635-48
17081983
Mol Syst Biol. 2009;5:237
19156129
Mol Cell. 2009 Apr 10;34(1):115-31
19362540
Nat Protoc. 2006;1(6):2856-60
17406544
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18902-7
19846766
Sci Signal. 2009 Aug 18;2(84):ra46
19690332
Mol Cell Proteomics. 2007 Mar;6(3):377-81
17164402
Diabetes. 2006 Aug;55(8):2171-9
16873679
Nat Chem Biol. 2005 Oct;1(5):252-62
16408053
PLoS Comput Biol. 2007 Jan 5;3(1):e4
17206861
Nat Methods. 2009 May;6(5):359-62
19377485
Cell. 2007 Jun 29;129(7):1415-26
17570479
Mol Cell. 2009 Oct 23;36(2):326-39
19854140
Science. 2010 Feb 19;327(5968):1004-7
20167787
J Proteome Res. 2009 Nov;8(11):5347-55
19754192
Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):692-7
18180459
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80
14681412
J Chromatogr B Analyt Technol Biomed Life Sci. 2009 May 1;877(13):1229-39
19041286
Nat Rev Mol Cell Biol. 2009 Sep;10(9):609-22
19696798
Mol Cell. 2007 Dec 14;28(5):730-8
18082598
Cell. 1996 Jun 14;85(6):817-27
8681377
Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7
18669648
Nature. 2009 Aug 6;460(7256):762-5
19606093
J Proteome Res. 2008 Dec;7(12):5314-26
19367708
Sci Signal. 2008 Sep 02;1(35):ra2
18765831
Sci Signal. 2010 Jan 12;3(104):ra2
20068230
Nat Biotechnol. 2004 Sep;22(9):1139-45
15314609
J Proteome Res. 2008 Mar;7(3):1118-30
18271523
Mol Cell Proteomics. 2008 Apr;7(4):672-83
18045802
Nat Methods. 2008 Jun;5(6):459-60
18511913
Mol Cell Proteomics. 2009 Mar;8(3):519-34
19001411
J Proteome Res. 2008 Jan;7(1):51-61
18173218