title: Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry.
abstract: Protein-protein interactions are important for nearly all biological processes, and it is known that aberrant protein-protein interactions can lead to human disease and cancer. Recent evidence has suggested that protein interaction interfaces describe a new class of attractive targets for drug development. Full characterization of protein interaction networks of protein complexes and their dynamics in response to various cellular cues will provide essential information for us to understand how protein complexes work together in cells to maintain cell viability and normal homeostasis. Affinity purification coupled with quantitative mass spectrometry has become the primary method for studying in vivo protein interactions of protein complexes and whole organism proteomes. Recent developments in sample preparation and affinity purification strategies allow the capture, identification, and quantification of protein interactions of protein complexes that are stable, dynamic, transient, and/or weak. Current efforts have mainly focused on generating reliable, reproducible, and high confidence protein interaction data sets for functional characterization. The availability of increasing amounts of information on protein interactions in eukaryotic systems and new bioinformatics tools allow functional analysis of quantitative protein interaction data to unravel the biological significance of the identified protein interactions. Existing studies in this area have laid a solid foundation toward generating a complete map of in vivo protein interaction networks of protein complexes in cells or tissues.
authors.affiliation: Department of Physiology and Biophysics, University of California, Irvine, California 92697-4560, USA.
authors.forename: Robyn M
authors.initials: RM
authors.lastname: Kaake
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Wang
authors.forename: Lan
authors.initials: L
authors.lastname: Huang
mesh_terms: D002846:Chromatography, Affinity / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D046912:Multiprotein Complexes / Q000378:metabolism*; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software
chemical_list: D046912:Multiprotein Complexes
references.citation: Curr Opin Struct Biol. 2000 Oct;10(5):601-6
references.pmid: 11042460
references.citation: Nat Methods. 2006 Dec;3(12):1013-9
references.pmid: 17060908
references.citation: BMC Bioinformatics. 2007 Nov 02;8:426
references.pmid: 17980028
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51
references.pmid: 14681454
references.citation: J Proteome Res. 2009 Jun;8(6):2944-52
references.pmid: 19317493
references.citation: Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18928-33
references.pmid: 17138671
references.citation: Methods Mol Biol. 2007;359:17-35
references.pmid: 17484108
references.citation: Mol Syst Biol. 2007;3:89
references.pmid: 17353931
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1454-9
references.pmid: 18218781
references.citation: Nucleic Acids Res. 1998 Jan 1;26(1):73-9
references.pmid: 9399804
references.citation: Mol Syst Biol. 2005;1:2005.0008
references.pmid: 16729043
references.citation: J Proteome Res. 2009 May;8(5):2211-7
references.pmid: 19338310
references.citation: Nat Biotechnol. 2010 Jan;28(1):40-2
references.pmid: 20062039
references.citation: J Proteome Res. 2006 Sep;5(9):2339-47
references.pmid: 16944946
references.citation: Nat Methods. 2009 Mar;6(3):203-5
references.pmid: 19198594
references.citation: Mol Cell Proteomics. 2003 May;2(5):299-314
references.pmid: 12766231
references.citation: J Mol Biol. 2010 Apr 30;398(2):200-13
references.pmid: 20226197
references.citation: Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
references.pmid: 10982861
references.citation: BMC Bioinformatics. 2006 Nov 06;7:488
references.pmid: 17087821
references.citation: Anal Bioanal Chem. 2010 Aug;397(8):3433-40
references.pmid: 20076950
references.citation: Nat Protoc. 2009;4(1):44-57
references.pmid: 19131956
references.citation: Mol Cell Proteomics. 2009 May;8(5):1150-64
references.pmid: 19193609
references.citation: Mol Cell Proteomics. 2008 Jan;7(1):15-34
references.pmid: 17934213
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19948-53
references.pmid: 18077427
references.citation: PLoS Comput Biol. 2009 Dec;5(12):e1000601
references.pmid: 20011507
references.citation: Mol Cell Proteomics. 2008 Feb;7(2):326-46
references.pmid: 17956857
references.citation: Nat Cell Biol. 2009 Dec;11(12):1458-64
references.pmid: 19935650
references.citation: Science. 2009 Nov 27;326(5957):1235-40
references.pmid: 19965468
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4
references.pmid: 17135203
references.citation: Nat Cell Biol. 2004 Feb;6(2):97-105
references.pmid: 14743216
references.citation: Proteomics. 2007 Oct;7(19):3470-80
references.pmid: 17726677
references.citation: Annu Rev Biochem. 2007;76:167-93
references.pmid: 17328674
references.citation: Nature. 2009 Oct 29;461(7268):1234-42
references.pmid: 19838167
references.citation: J Physiol. 2005 Feb 15;563(Pt 1):11-21
references.pmid: 15611014
references.citation: J Cell Biol. 2008 Oct 20;183(2):223-39
references.pmid: 18936248
references.citation: Methods. 1999 Feb;17(2):125-39
references.pmid: 10075891
references.citation: Cell. 2009 Jul 23;138(2):389-403
references.pmid: 19615732
references.citation: Biochem J. 2010 Jan 15;425(3):489-500
references.pmid: 20070258
references.citation: Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2431-6
references.pmid: 20133760
references.citation: Biotechnol Annu Rev. 2008;14:1-28
references.pmid: 18606358
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13333-8
references.pmid: 18757749
references.citation: Bioinformatics. 2006 Apr 15;22(8):1021-3
references.pmid: 16473872
references.citation: Science. 2007 May 18;316(5827):1043-6
references.pmid: 17510365
references.citation: Nat Rev Mol Cell Biol. 2006 Dec;7(12):952-8
references.pmid: 17139335
references.citation: J Proteome Res. 2006 Jan;5(1):64-75
references.pmid: 16396496
references.citation: Mol Cell Proteomics. 2009 Jan;8(1):157-71
references.pmid: 18782753
references.citation: Mol Cell. 2009 Oct 9;36(1):141-52
references.pmid: 19818717
references.citation: Mol Cell Proteomics. 2010 Jan;9(1):11-24
references.pmid: 19955089
references.citation: J Am Chem Soc. 2007 Oct 24;129(42):12809-14
references.pmid: 17902662
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24
references.pmid: 15608229
references.citation: Nat Biotechnol. 2003 Mar;21(3):315-8
references.pmid: 12577067
references.citation: Mol Cell Proteomics. 2008 May;7(5):845-52
references.pmid: 18087068
references.citation: Nat Methods. 2006 Dec;3(12):981-3
references.pmid: 17072306
references.citation: Nature. 2002 Jan 10;415(6868):180-3
references.pmid: 11805837
references.citation: Bioinformatics. 2005 Sep 15;21(18):3587-95
references.pmid: 15994189
references.citation: FEBS Lett. 2008 Apr 9;582(8):1220-4
references.pmid: 18282471
references.citation: Nature. 2006 Mar 30;440(7084):637-43
references.pmid: 16554755
references.citation: Genome Res. 2003 Oct;13(10):2363-71
references.pmid: 14525934
references.citation: J Proteome Res. 2008 Apr;7(4):1740-9
references.pmid: 18327965
references.citation: J Mass Spectrom. 2008 Jun;43(6):699-715
references.pmid: 18438963
references.citation: J Proteome Res. 2003 Mar-Apr;2(2):173-81
references.pmid: 12716131
references.citation: Nat Methods. 2007 Oct;4(10):787-97
references.pmid: 17901868
references.citation: Nature. 2008 May 22;453(7194):548-52
references.pmid: 18497827
references.citation: Nat Methods. 2009 Jan;6(1):75-7
references.pmid: 19079255
references.citation: Mol Cell Proteomics. 2005 Oct;4(10):1487-502
references.pmid: 15979981
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
references.pmid: 17145710
references.citation: Nature. 2003 Dec 4;426(6966):570-4
references.pmid: 14654843
references.citation: Proteomics. 2008 Jun;8(12):2366-70
references.pmid: 18563728
references.citation: Bioinformatics. 2009 Dec 1;25(23):3143-50
references.pmid: 19770263
references.citation: Nat Methods. 2007 Oct;4(10):807-15
references.pmid: 17901870
references.citation: PLoS One. 2009 Oct 06;4(10):e7310
references.pmid: 19806189
references.citation: Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54
references.pmid: 17593931
references.citation: Nature. 2002 Jan 10;415(6868):141-7
references.pmid: 11805826
references.citation: Nature. 2006 Mar 30;440(7084):631-6
references.pmid: 16429126
references.citation: Genome Res. 2004 Jun;14(6):1170-5
references.pmid: 15140827
references.citation: IEEE Trans Neural Netw. 2005 May;16(3):645-78
references.pmid: 15940994
references.citation: Mol Cell Proteomics. 2007 Feb;6(2):252-71
references.pmid: 17052974
references.citation: Bioinformatics. 2004 Oct 12;20(15):2466-70
references.pmid: 15117749
references.citation: Mol Cell Proteomics. 2010 Jun;9(6):1144-56
references.pmid: 20097687
references.citation: J Biol Chem. 2009 Dec 4;284(49):33713-8
references.pmid: 19812037
references.citation: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references.pmid: 15385600
references.citation: Proteomics. 2009 Dec;9(24):5414-24
references.pmid: 19834888
references.citation: Clin Cancer Res. 2008 Sep 1;14(17):5318-24
references.pmid: 18765522
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D436-41
references.pmid: 16381906
references.citation: Annu Rev Pharmacol Toxicol. 2010;50:131-56
references.pmid: 20055700
references.citation: Ernst Schering Found Symp Proc. 2008;(1):75-97
references.pmid: 19198065
references.citation: Adv Biochem Eng Biotechnol. 2008;110:1-24
references.pmid: 18219467
references.citation: Curr Opin Biotechnol. 2008 Aug;19(4):331-7
references.pmid: 18590817
references.citation: Nat Biotechnol. 1999 Oct;17(10):994-9
references.pmid: 10504701
references.citation: Nat Biotechnol. 2004 Jun;22(6):724-31
references.pmid: 15146195
references.citation: J Proteome Res. 2008 Nov;7(11):4914-25
references.pmid: 18850735
references.citation: Mol Cell Proteomics. 2002 May;1(5):376-86
references.pmid: 12118079
references.citation: Cell Cycle. 2010 Mar 15;9(6):1104-11
references.pmid: 20237429
references.citation: Proteome Sci. 2009 Dec 24;7:46
references.pmid: 20034391
references.citation: Nat Biotechnol. 2010 Jan;28(1):83-9
references.pmid: 20010810
references.citation: Cell. 2009 Apr 3;137(1):133-45
references.pmid: 19345192
references.citation: J Proteome Res. 2009 Mar;8(3):1504-14
references.pmid: 19206470
references.citation: Oncogene. 2010 Jan 7;29(1):1-10
references.pmid: 19826416
references.citation: Bioinformatics. 2010 Jan 1;26(1):77-83
references.pmid: 19861354
references.citation: Nat Biotechnol. 2007 Mar;25(3):345-52
references.pmid: 17322870
references.citation: Mol Cell Proteomics. 2005 Apr;4(4):545-54
references.pmid: 15695425
references.citation: Proteomics. 2004 Dec;4(12):3845-54
references.pmid: 15540166
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7414-9
references.pmid: 19380743
references.citation: Mol Cell Proteomics. 2005 Dec;4(12):1933-41
references.pmid: 16155292
references.citation: Mol Cell Proteomics. 2008 Jan;7(1):46-57
references.pmid: 17934176
references.citation: Bioinformatics. 2008 Jul 1;24(13):1556-8
references.pmid: 18453552
references.citation: Mol Cell. 2009 May 15;34(3):354-63
references.pmid: 19450533
references.citation: J Proteome Res. 2005 Sep-Oct;4(5):1752-6
references.pmid: 16212429
references.citation: Mol Cell Proteomics. 2006 Apr;5(4):737-48
references.pmid: 16432255
references.citation: EMBO J. 2010 Feb 17;29(4):717-26
references.pmid: 20094031
references.citation: Science. 2004 Mar 26;303(5666):2026-9
references.pmid: 15044803
references.citation: Curr Opin Chem Biol. 2003 Feb;7(1):21-7
references.pmid: 12547422
references.citation: FEBS Lett. 2009 Jun 5;583(11):1674-83
references.pmid: 19376113
references.citation: Cell. 1998 Feb 6;92(3):291-4
references.pmid: 9476889
references.citation: Nat Rev Genet. 2009 Sep;10(9):617-27
references.pmid: 19687803
references.citation: BMC Bioinformatics. 2006 Apr 14;7:207
references.pmid: 16613608
references.citation: Proteomics. 2005 Jan;5(1):4-15
references.pmid: 15602776
references.citation: Mol Cell Proteomics. 2006 Feb;5(2):366-78
references.pmid: 16284124
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
references.pmid: 18940858
references.citation: Proteomics. 2009 Oct;9(20):4590-605
references.pmid: 19743428
references.citation: J Proteome Res. 2010 Apr 5;9(4):2016-29
references.pmid: 20170199
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40
references.pmid: 18000002