Home LiteratureArticle Details
PMID: 23157382 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions.

Analytical chemistry ·Vol. 85 ·No. 2 ·2013-01-15 ·Pages 749-68

Miteva YV, Budayeva HG, Cristea IM

Abstract

暂无摘要

MeSH Terms
Animals Humans Protein Binding Proteins/chemistry Proteomics
Chemicals
Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Miteva Yana V
210 Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
Budayeva Hanna G
Cristea Ileana M
References (243)
243 references, click to expand
  1. Proteomics: a pragmatic perspective.
    Nat Biotechnol. 2010 Jul;28(7):695-709 PMID: 20622844
  2. Recent advances in charting protein-protein interaction: mass spectrometry-based approaches.
    Curr Opin Biotechnol. 2011 Feb;22(1):42-9 PMID: 20934865
  3. Cytoscape 2.8: new features for data integration and network visualization.
    Bioinformatics. 2011 Feb 1;27(3):431-2 PMID: 21149340
  4. Protein solubilization: attend to the choice of lysis buffer.
    Methods Mol Biol. 2012;869:37-47 PMID: 22585475
  5. Network visualization and analysis of gene expression data using BioLayout Express(3D).
    Nat Protoc. 2009;4(10):1535-50 PMID: 19798086
  6. Purification and characterization of an active N-acetylglucosaminyltransferase enzyme complex from Streptococci.
    Appl Environ Microbiol. 2010 Dec;76(24):7966-71 PMID: 20971868
  7. The Database of Interacting Proteins: 2004 update.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51 PMID: 14681454
  8. Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry.
    Proteomics. 2011 Dec;11(23):4514-28 PMID: 21932443
  9. Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides.
    Mol Cell Proteomics. 2010 Jan;9(1):25-31 PMID: 19809093
  10. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors.
    Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18928-33 PMID: 17138671
  11. ReCLIP (reversible cross-link immuno-precipitation): an efficient method for interrogation of labile protein complexes.
    PLoS One. 2011 Jan 20;6(1):e16206 PMID: 21283770
  12. Global analysis of protein localization in budding yeast.
    Nature. 2003 Oct 16;425(6959):686-91 PMID: 14562095
  13. HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.
    BMC Bioinformatics. 2005 Dec 01;6 Suppl 4:S21 PMID: 16351748
  14. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.
    Mol Cell Proteomics. 2011 Jun;10(6):M110.006478 PMID: 21454883
  15. The influenza A virus NS1 protein interacts with the nucleoprotein of viral ribonucleoprotein complexes.
    J Virol. 2011 May;85(10):5228-31 PMID: 21411538
  16. Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition.
    Methods Mol Biol. 2007;359:17-35 PMID: 17484108
  17. CORUM: the comprehensive resource of mammalian protein complexes--2009.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D497-501 PMID: 19884131
  18. Large-scale mapping of human protein-protein interactions by mass spectrometry.
    Mol Syst Biol. 2007;3:89 PMID: 17353931
  19. Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics.
    Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1454-9 PMID: 18218781
  20. High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes.
    Methods. 2009 Aug;48(4):381-6 PMID: 19450687
  21. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
    Bioinformatics. 2009 Apr 15;25(8):1091-3 PMID: 19237447
  22. MSMEG_2731, an uncharacterized nucleic acid binding protein from Mycobacterium smegmatis, physically interacts with RPS1.
    PLoS One. 2012;7(5):e36666 PMID: 22590585
  23. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.
    Mol Cell Proteomics. 2010 Aug;9(8):1634-49 PMID: 20360032
  24. Tracking and elucidating alphavirus-host protein interactions.
    J Biol Chem. 2006 Oct 6;281(40):30269-78 PMID: 16895903
  25. Affinity isolation and I-DIRT mass spectrometric analysis of the Escherichia coli O157:H7 Sakai RNA polymerase complex.
    J Bacteriol. 2008 Feb;190(4):1284-9 PMID: 18083804
  26. Bacteriome.org--an integrated protein interaction database for E. coli.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D632-6 PMID: 17942431
  27. SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments.
    J Proteome Res. 2012 Apr 6;11(4):2619-24 PMID: 22352807
  28. A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation.
    Mol Cell Proteomics. 2010 May;9(5):851-60 PMID: 20023299
  29. STRING: a database of predicted functional associations between proteins.
    Nucleic Acids Res. 2003 Jan 1;31(1):258-61 PMID: 12519996
  30. Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase.
    Cell Res. 2011 Aug;21(8):1172-81 PMID: 21606950
  31. Isotopically labeled crosslinking reagents: resolution of mass degeneracy in the identification of crosslinked peptides.
    Bioorg Med Chem Lett. 2003 Nov 17;13(22):4023-6 PMID: 14592499
  32. Global landscape of HIV-human protein complexes.
    Nature. 2011 Dec 21;481(7381):365-70 PMID: 22190034
  33. Mapping spatial proximities of sulfhydryl groups in proteins using a fluorogenic cross-linker and mass spectrometry.
    Anal Biochem. 2004 Aug 1;331(1):27-32 PMID: 15245993
  34. An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine.
    PLoS One. 2011;6(10):e26044 PMID: 22022502
  35. Genetic and biochemical evaluation of the importance of Cdc6 in regulating mitotic exit.
    Mol Biol Cell. 2003 Nov;14(11):4592-604 PMID: 12960422
  36. The in vivo brain interactome of the amyloid precursor protein.
    Mol Cell Proteomics. 2008 Jan;7(1):15-34 PMID: 17934213
  37. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
    BMC Biol. 2007 Oct 09;5:44 PMID: 17925023
  38. Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus.
    J Virol. 2012 Jul;86(13):7360-71 PMID: 22553322
  39. The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification.
    Protein Expr Purif. 2010 Aug;72(2):149-56 PMID: 20399864
  40. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes.
    J Struct Biol. 2011 Mar;173(3):530-40 PMID: 21029779
  41. Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse.
    PLoS Biol. 2009 Apr 14;7(4):e83 PMID: 19402746
  42. Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking.
    Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19948-53 PMID: 18077427
  43. In vivo protein complex topologies: sights through a cross-linking lens.
    Proteomics. 2012 May;12(10):1565-75 PMID: 22610688
  44. CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins.
    Mol Cell Proteomics. 2008 Apr;7(4):739-49 PMID: 18281724
  45. Protein interactions of phosphatase and tensin homologue (PTEN) and its cancer-associated G20E mutant compared by using stable isotope labeling by amino acids in cell culture-based parallel affinity purification.
    J Biol Chem. 2011 May 20;286(20):18093-103 PMID: 21454687
  46. Resolving the composition of protein complexes using a MALDI LTQ Orbitrap.
    J Am Soc Mass Spectrom. 2010 Jan;21(1):34-46 PMID: 19822444
  47. Probability-based protein identification by searching sequence databases using mass spectrometry data.
    Electrophoresis. 1999 Dec;20(18):3551-67 PMID: 10612281
  48. Differential 14-3-3 affinity capture reveals new downstream targets of phosphatidylinositol 3-kinase signaling.
    Mol Cell Proteomics. 2009 Nov;8(11):2487-99 PMID: 19648646
  49. False discovery rate estimation for cross-linked peptides identified by mass spectrometry.
    Nat Methods. 2012 Sep;9(9):901-3 PMID: 22772729
  50. MINT: the Molecular INTeraction database.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4 PMID: 17135203
  51. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies.
    Nat Methods. 2008 Feb;5(2):163-5 PMID: 18176569
  52. Trends in ultrasensitive proteomics.
    Curr Opin Chem Biol. 2012 Apr;16(1-2):206-13 PMID: 22226769
  53. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
    Bioinformatics. 2010 Nov 15;26(22):2927-8 PMID: 20926419
  54. The molecular architecture of the nuclear pore complex.
    Nature. 2007 Nov 29;450(7170):695-701 PMID: 18046406
  55. The protein-protein interaction map of Helicobacter pylori.
    Nature. 2001 Jan 11;409(6817):211-5 PMID: 11196647
  56. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells.
    Nat Methods. 2006 Dec;3(12):1013-9 PMID: 17060908
  57. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.
    Nucleic Acids Res. 2009 Jul;37(Web Server issue):W115-21 PMID: 19465394
  58. The biochemical anatomy of cortical inhibitory synapses.
    PLoS One. 2012;7(6):e39572 PMID: 22768092
  59. Identification of novel protein kinase A phosphorylation sites in the M-domain of human and murine cardiac myosin binding protein-C using mass spectrometry analysis.
    J Proteome Res. 2010 Apr 5;9(4):1843-53 PMID: 20151718
  60. Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry.
    Methods Mol Biol. 2011;781:31-45 PMID: 21877275
  61. IntAct: an open source molecular interaction database.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5 PMID: 14681455
  62. Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data.
    Proteomics. 2010 May;10(9):1880-5 PMID: 20198642
  63. Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry.
    Anal Chem. 2008 Jul 1;80(13):4807-19 PMID: 18517224
  64. Aurora B-dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation.
    Mol Cell Proteomics. 2012 Nov;11(11):1220-9 PMID: 22865920
  65. Arena3D: visualizing time-driven phenotypic differences in biological systems.
    BMC Bioinformatics. 2012 Mar 22;13:45 PMID: 22439608
  66. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes.
    J Cell Biol. 2008 Oct 20;183(2):223-39 PMID: 18936248
  67. Defining the human deubiquitinating enzyme interaction landscape.
    Cell. 2009 Jul 23;138(2):389-403 PMID: 19615732
  68. Tandem affinity purification of protein complexes from mammalian cells by the Strep/FLAG (SF)-TAP tag.
    Methods Mol Biol. 2009;564:359-72 PMID: 19544034
  69. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
    Bioinformatics. 2004 Dec 12;20(18):3710-5 PMID: 15297299
  70. A conserved protein network controls assembly of the outer kinetochore and its ability to sustain tension.
    Genes Dev. 2004 Sep 15;18(18):2255-68 PMID: 15371340
  71. MIPS: analysis and annotation of proteins from whole genomes.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D41-4 PMID: 14681354
  72. Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells.
    Nat Methods. 2005 Apr;2(4):261-7 PMID: 15782218
  73. Structure-function mapping of a heptameric module in the nuclear pore complex.
    J Cell Biol. 2012 Feb 20;196(4):419-34 PMID: 22331846
  74. Streamlined analysis schema for high-throughput identification of endogenous protein complexes.
    Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2431-6 PMID: 20133760
  75. Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs.
    J Proteome Res. 2010 May 7;9(5):2488-95 PMID: 20349954
  76. Shotgun cross-linking analysis for studying quaternary and tertiary protein structures.
    J Proteome Res. 2007 Oct;6(10):3908-17 PMID: 17854217
  77. Mapping the local protein interactome of the NuA3 histone acetyltransferase.
    Protein Sci. 2009 Sep;18(9):1987-97 PMID: 19621382
  78. Collision-induced dissociative chemical cross-linking reagents and methodology: Applications to protein structural characterization using tandem mass spectrometry analysis.
    Anal Chem. 2006 Dec 1;78(23):8059-68 PMID: 17134140
  79. Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein.
    J Virol. 2010 Aug;84(15):7803-14 PMID: 20504932
  80. Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes.
    Mol Cell Proteomics. 2005 Aug;4(8):1167-79 PMID: 15901824
  81. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels.
    Biotechniques. 2012 May;0(0):1-6 PMID: 22668517
  82. MPIDB: the microbial protein interaction database.
    Bioinformatics. 2008 Aug 1;24(15):1743-4 PMID: 18556668
  83. Interactive three-dimensional visualization and contextual analysis of protein interaction networks.
    J Proteome Res. 2008 Jan;7(1):104-12 PMID: 18020406
  84. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3.
    Mol Cell Biol. 2011 Jul;31(13):2641-52 PMID: 21555454
  85. Nucleophosmin (NPM1/B23) interacts with activating transcription factor 5 (ATF5) protein and promotes proteasome- and caspase-dependent ATF5 degradation in hepatocellular carcinoma cells.
    J Biol Chem. 2012 Jun 1;287(23):19599-609 PMID: 22528486
  86. Efficient and non-denaturing membrane solubilization combined with enrichment of membrane protein complexes by detergent/polymer aqueous two-phase partitioning for proteome analysis.
    J Chromatogr A. 2006 Jul 28;1122(1-2):35-46 PMID: 16682048
  87. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
    Bioinformatics. 2004 Mar 1;20(4):578-80 PMID: 14990455
  88. A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies.
    Mol Biosyst. 2010 Jun;6(6):939-47 PMID: 20485738
  89. Selective enrichment of azide-containing peptides from complex mixtures.
    J Proteome Res. 2009 Jul;8(7):3702-11 PMID: 19402736
  90. A QUICK screen for Lrrk2 interaction partners--leucine-rich repeat kinase 2 is involved in actin cytoskeleton dynamics.
    Mol Cell Proteomics. 2011 Jan;10(1):M110.001172 PMID: 20876399
  91. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5 PMID: 22121212
  92. Preparation of multiprotein complexes from Arabidopsis chloroplasts using tandem affinity purification.
    Methods Mol Biol. 2011;775:31-49 PMID: 21863437
  93. The Biomolecular Interaction Network Database and related tools 2005 update.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24 PMID: 15608229
  94. Bimolecular affinity purification (BAP): tandem affinity purification using two protein baits.
    Cold Spring Harb Protoc. 2009 Nov;2009(11):pdb.prot5318 PMID: 20150057
  95. A novel tandem affinity purification strategy for the efficient isolation and characterisation of native protein complexes.
    Proteomics. 2007 Dec;7(23):4228-34 PMID: 17979178
  96. Recombineering BAC transgenes for protein tagging.
    Methods. 2011 Feb;53(2):113-9 PMID: 20868752
  97. Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions.
    J Am Soc Mass Spectrom. 2010 Jun;21(6):1050-60 PMID: 20207164
  98. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.
    Database (Oxford). 2010 Aug 05;2010:baq019 PMID: 20689020
  99. DAVID: Database for Annotation, Visualization, and Integrated Discovery.
    Genome Biol. 2003;4(5):P3 PMID: 12734009
  100. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).
    Nat Methods. 2006 Dec;3(12):981-3 PMID: 17072306
  101. Commonly used tag combinations for tandem affinity purification.
    Biotechnol Appl Biochem. 2010 Feb 15;55(2):73-83 PMID: 20156193
  102. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.
    Nature. 2011 Dec 21;481(7381):371-5 PMID: 22190037
  103. Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation.
    Mol Cell Proteomics. 2011 Feb;10(2):M110.004317 PMID: 21081666
  104. Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions.
    J Proteome Res. 2008 Mar;7(3):1244-50 PMID: 18271525
  105. A genomic perspective on protein families.
    Science. 1997 Oct 24;278(5338):631-7 PMID: 9381173
  106. Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16.
    Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10558-63 PMID: 22691496
  107. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
    Nature. 2006 Mar 30;440(7084):637-43 PMID: 16554755
  108. Pol β associated complex and base excision repair factors in mouse fibroblasts.
    Nucleic Acids Res. 2012 Dec;40(22):11571-82 PMID: 23042675
  109. Development of human protein reference database as an initial platform for approaching systems biology in humans.
    Genome Res. 2003 Oct;13(10):2363-71 PMID: 14525934
  110. Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes.
    Mol Cell Proteomics. 2011 Jan;10(1):M110.002212 PMID: 20736410
  111. Alternative affinity tools: more attractive than antibodies?
    Biochem J. 2011 May 15;436(1):1-13 PMID: 21524274
  112. Immunoisolation of protein complexes from Xenopus.
    Methods Mol Biol. 2012;917:369-90 PMID: 22956099
  113. MatrixDB, the extracellular matrix interaction database.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D235-40 PMID: 20852260
  114. Navigating the deubiquitinating proteome with a CompPASS.
    Cell. 2009 Jul 23;138(2):222-4 PMID: 19632171
  115. Mass spectrometry and protein analysis.
    Science. 2006 Apr 14;312(5771):212-7 PMID: 16614208
  116. Human immunodeficiency virus type 1, human protein interaction database at NCBI.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D417-22 PMID: 18927109
  117. Integrated network analysis platform for protein-protein interactions.
    Nat Methods. 2009 Jan;6(1):75-7 PMID: 19079255
  118. The Protein Information Resource.
    Nucleic Acids Res. 2003 Jan 1;31(1):345-7 PMID: 12520019
  119. Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes.
    Anal Chem. 2010 Aug 1;82(15):6643-51 PMID: 20614870
  120. Mapping protein interactions between Dengue virus and its human and insect hosts.
    PLoS Negl Trop Dis. 2011 Feb 15;5(2):e954 PMID: 21358811
  121. Global analysis of Cdc14 phosphatase reveals diverse roles in mitotic processes.
    J Biol Chem. 2011 Feb 18;286(7):5434-45 PMID: 21127052
  122. Mass spectrometry in the postgenomic era.
    Annu Rev Biochem. 2011;80:239-46 PMID: 21675917
  123. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
    Mol Cell Proteomics. 2007 Mar;6(3):439-50 PMID: 17200106
  124. Native protein mass spectrometry: from intact oligomers to functional machineries.
    Curr Opin Chem Biol. 2004 Oct;8(5):519-26 PMID: 15450495
  125. Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry.
    Proteomics. 2012 May;12(10):1623-38 PMID: 22610586
  126. Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique.
    Anal Chem. 2010 Apr 1;82(7):2636-42 PMID: 20210330
  127. Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data.
    Proteomics. 2003 Jun;3(6):870-8 PMID: 12833510
  128. Epitope tagging of endogenous proteins for genome-wide chromatin immunoprecipitation analysis.
    Methods Mol Biol. 2009;567:87-98 PMID: 19588087
  129. A global protein kinase and phosphatase interaction network in yeast.
    Science. 2010 May 21;328(5981):1043-6 PMID: 20489023
  130. Proteome survey reveals modularity of the yeast cell machinery.
    Nature. 2006 Mar 30;440(7084):631-6 PMID: 16429126
  131. Isolation and characterization of plant protein complexes by mass spectrometry.
    Proteomics. 2011 May;11(9):1824-33 PMID: 21472857
  132. Isotope-coded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces.
    J Am Chem Soc. 2006 Aug 16;128(32):10362-3 PMID: 16895390
  133. Stepwise evolution of protein native structure with electrospray into the gas phase, 10(-12) to 10(2) s.
    Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18145-52 PMID: 19033474
  134. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes.
    Nat Biotechnol. 2011 Mar;29(3):255-65 PMID: 21258344
  135. ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite.
    BMC Bioinformatics. 2010 Jan 28;11:64 PMID: 20109223
  136. Mapping intact protein isoforms in discovery mode using top-down proteomics.
    Nature. 2011 Oct 30;480(7376):254-8 PMID: 22037311
  137. Systematic analysis of human protein complexes identifies chromosome segregation proteins.
    Science. 2010 Apr 30;328(5978):593-9 PMID: 20360068
  138. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.
    Anal Chem. 2009 Jul 1;81(13):5524-32 PMID: 19496583
  139. Mass spectrometry-based proteomics in cell biology.
    J Cell Biol. 2010 Aug 23;190(4):491-500 PMID: 20733050
  140. Analysis of the human endogenous coregulator complexome.
    Cell. 2011 May 27;145(5):787-99 PMID: 21620140
  141. HPID: the Human Protein Interaction Database.
    Bioinformatics. 2004 Oct 12;20(15):2466-70 PMID: 15117749
  142. A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes.
    J Am Soc Mass Spectrom. 2001 Feb;12(2):222-7 PMID: 11212007
  143. xComb: a cross-linked peptide database approach to protein-protein interaction analysis.
    J Proteome Res. 2010 May 7;9(5):2508-15 PMID: 20302351
  144. Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays.
    Proteomics. 2012 May;12(10):1499-518 PMID: 22589225
  145. Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes.
    Annu Rev Biochem. 2011;80:247-71 PMID: 21548785
  146. Affinity chromatography as a tool for antibody purification.
    Methods. 2012 Feb;56(2):116-29 PMID: 22033471
  147. Identification of cross-linked peptides from large sequence databases.
    Nat Methods. 2008 Apr;5(4):315-8 PMID: 18327264
  148. A gene network for navigating the literature.
    Nat Genet. 2004 Jul;36(7):664 PMID: 15226743
  149. GoMiner: a resource for biological interpretation of genomic and proteomic data.
    Genome Biol. 2003;4(4):R28 PMID: 12702209
  150. Examining the complexity of human RNA polymerase complexes using HaloTag technology coupled to label free quantitative proteomics.
    J Proteome Res. 2012 Feb 3;11(2):564-75 PMID: 22149079
  151. Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA.
    PLoS Pathog. 2010 Jun 24;6(6):e1000965 PMID: 20585571
  152. Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry.
    Mol Cell Proteomics. 2010 Aug;9(8):1650-65 PMID: 20445003
  153. The GOA database in 2009--an integrated Gene Ontology Annotation resource.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403 PMID: 18957448
  154. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.
    Mol Cell Proteomics. 2004 Dec;3(12):1154-69 PMID: 15385600
  155. The IntAct molecular interaction database in 2012.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6 PMID: 22121220
  156. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.
    J Proteome Res. 2012 May 4;11(5):2968-81 PMID: 22390342
  157. MPact: the MIPS protein interaction resource on yeast.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D436-41 PMID: 16381906
  158. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.
    Proc Natl Acad Sci U S A. 2000 May 23;97(11):5802-6 PMID: 10811876
  159. Four-dimensional visualisation and analysis of protein-protein interaction networks.
    Proteomics. 2011 Jul;11(13):2672-82 PMID: 21630449
  160. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.
    Bioinformatics. 2005 Aug 15;21(16):3448-9 PMID: 15972284
  161. SCOPPI: a structural classification of protein-protein interfaces.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D310-4 PMID: 16381874
  162. Mass spectrometry of intracellular and membrane proteins using cleavable detergents.
    Anal Chem. 2003 Dec 1;75(23):6642-7 PMID: 14640740
  163. Isolation of the silicatein-α interactor silintaphin-2 by a novel solid-phase pull-down assay.
    Biochemistry. 2011 Mar 29;50(12):1981-90 PMID: 21319729
  164. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.
    Mol Cell. 2007 Jul 20;27(2):262-74 PMID: 17643375
  165. Hepatitis B virus encoded X protein suppresses apoptosis by inhibition of the caspase-independent pathway.
    J Proteome Res. 2012 Oct 5;11(10):4803-13 PMID: 22871131
  166. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans.
    Sci STKE. 2005 Jan 11;2005(266):pl1 PMID: 15644491
  167. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
    Nat Biotechnol. 1999 Oct;17(10):994-9 PMID: 10504701
  168. Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues.
    Nat Biotechnol. 2004 Jun;22(6):724-31 PMID: 15146195
  169. A docking model based on mass spectrometric and biochemical data describes phage packaging motor incorporation.
    Mol Cell Proteomics. 2010 Aug;9(8):1764-73 PMID: 20124351
  170. Predictome: a database of putative functional links between proteins.
    Nucleic Acids Res. 2002 Jan 1;30(1):306-9 PMID: 11752322
  171. Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma.
    Mol Cell. 2009 Apr 10;34(1):115-31 PMID: 19362540
  172. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry.
    Science. 2012 Sep 14;337(6100):1348-52 PMID: 22984071
  173. MitoP2: the mitochondrial proteome database--now including mouse data.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D705-11 PMID: 16381964
  174. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors.
    Nat Biotechnol. 2007 Sep;25(9):1035-44 PMID: 17721511
  175. New insights into the functions and localization of nuclear CCT protein complex in K562 leukemia cells.
    Proteomics Clin Appl. 2012 Oct;6(9-10):467-75 PMID: 22821915
  176. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.
    Mol Cell Proteomics. 2002 May;1(5):376-86 PMID: 12118079
  177. A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins.
    Mol Cell Proteomics. 2008 Feb;7(2):282-9 PMID: 17951627
  178. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.
    Nature. 2012 Sep 27;489(7417):585-9 PMID: 22940862
  179. Cross-linking measurements of in vivo protein complex topologies.
    Mol Cell Proteomics. 2011 Oct;10(10):M110.006841 PMID: 21697552
  180. The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase.
    J Bacteriol. 2010 Jul;192(14):3713-21 PMID: 20472786
  181. Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry.
    Mol Cell Proteomics. 2009 Mar;8(3):409-20 PMID: 18936057
  182. Systematic identification of interactions between host cell proteins and E7 oncoproteins from diverse human papillomaviruses.
    Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):E260-7 PMID: 22232672
  183. Analysis of stable and transient protein-protein interactions.
    Methods Mol Biol. 2012;833:143-52 PMID: 22183593
  184. Protein cross-links: universal isolation and characterization by isotopic derivatization and electrospray ionization mass spectrometry.
    Anal Biochem. 1999 Sep 10;273(2):192-203 PMID: 10469490
  185. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.
    Nat Methods. 2008 May;5(5):409-15 PMID: 18391959
  186. Identification of cross-linked peptides from complex samples.
    Nat Methods. 2012 Sep;9(9):904-6 PMID: 22772728
  187. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D736-43 PMID: 21036869
  188. Characterization of protein cross-links via mass spectrometry and an open-modification search strategy.
    Anal Chem. 2008 Nov 15;80(22):8799-806 PMID: 18947195
  189. Improved elution conditions for native co-immunoprecipitation.
    PLoS One. 2011 Mar 23;6(3):e18218 PMID: 21448433
  190. Mass spectrometry characterization of multiprotein complexes.
    Cold Spring Harb Protoc. 2009 Mar;2009(3):pdb.prot5180 PMID: 20147115
  191. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry.
    Anal Chem. 2000 Jan 15;72(2):267-75 PMID: 10658319
  192. Assessing the components of the eIF3 complex and their phosphorylation status.
    J Proteome Res. 2011 Apr 1;10(4):1481-94 PMID: 21280672
  193. Systematic identification of the HSP90 candidate regulated proteome.
    Mol Cell Proteomics. 2012 Jun;11(6):M111.016675 PMID: 22337586
  194. Mass spectrometry identifiable cross-linking strategy for studying protein-protein interactions.
    Anal Chem. 2005 Jan 1;77(1):311-8 PMID: 15623310
  195. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks.
    Nat Biotechnol. 2007 Mar;25(3):345-52 PMID: 17322870
  196. Accurate quantitation of protein expression and site-specific phosphorylation.
    Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6591-6 PMID: 10359756
  197. QUICK identification and SPR validation of signal transducers and activators of transcription 3 (Stat3) interacting proteins.
    J Proteomics. 2012 Jan 4;75(3):1055-66 PMID: 22075167
  198. Universal sample preparation method for proteome analysis.
    Nat Methods. 2009 May;6(5):359-62 PMID: 19377485
  199. The BioGRID Interaction Database: 2011 update.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704 PMID: 21071413
  200. Structural organization of the 19S proteasome lid: insights from MS of intact complexes.
    PLoS Biol. 2006 Aug;4(8):e267 PMID: 16869714
  201. In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry.
    Mol Cell Proteomics. 2011 Jun;10(6):M110.002386 PMID: 21447707
  202. Fluorescent proteins as proteomic probes.
    Mol Cell Proteomics. 2005 Dec;4(12):1933-41 PMID: 16155292
  203. Ongoing and future developments at the Universal Protein Resource.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9 PMID: 21051339
  204. Identifying dynamic interactors of protein complexes by quantitative mass spectrometry.
    Mol Cell Proteomics. 2008 Jan;7(1):46-57 PMID: 17934176
  205. Fluorescent protein specific Nanotraps to study protein-protein interactions and histone-tail peptide binding.
    Methods Mol Biol. 2012;911:475-83 PMID: 22886270
  206. Two-dimensional Blue native/SDS gel electrophoresis of multi-protein complexes from whole cellular lysates: a proteomics approach.
    Mol Cell Proteomics. 2004 Feb;3(2):176-82 PMID: 14665681
  207. Defining human ERAD networks through an integrative mapping strategy.
    Nat Cell Biol. 2011 Nov 27;14(1):93-105 PMID: 22119785
  208. Structural analysis of multiprotein complexes by cross-linking, mass spectrometry, and database searching.
    Mol Cell Proteomics. 2007 Dec;6(12):2200-11 PMID: 17921176
  209. Online predicted human interaction database.
    Bioinformatics. 2005 May 1;21(9):2076-82 PMID: 15657099
  210. Co-immunoprecipitation of protein complexes.
    Methods Mol Med. 2007;131:103-11 PMID: 17656778
  211. Medusa: a simple tool for interaction graph analysis.
    Bioinformatics. 2005 Dec 15;21(24):4432-3 PMID: 16188923
  212. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions.
    J Proteome Res. 2005 Sep-Oct;4(5):1752-6 PMID: 16212429
  213. Multiple tandem epitope tagging for enhanced detection of protein expressed in mammalian cells.
    Mol Biotechnol. 2001 Nov;19(3):313-21 PMID: 11721627
  214. A novel calmodulin-β-PIX interaction and its implication in receptor tyrosine kinase regulation.
    Cell Signal. 2012 Sep;24(9):1790-6 PMID: 22588125
  215. Distinct factors control histone variant H3.3 localization at specific genomic regions.
    Cell. 2010 Mar 5;140(5):678-91 PMID: 20211137
  216. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
    EMBO J. 2010 Feb 17;29(4):717-26 PMID: 20094031
  217. Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B.
    J Biol Chem. 2011 Feb 18;286(7):5012-22 PMID: 21127351
  218. Curating the innate immunity interactome.
    BMC Syst Biol. 2010 Aug 20;4:117 PMID: 20727158
  219. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription.
    Mol Cell Proteomics. 2012 May;11(5):60-76 PMID: 22586326
  220. Proteomic characterization of pseudorabies virus extracellular virions.
    J Virol. 2011 Jul;85(13):6427-41 PMID: 21525350
  221. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies.
    Anal Chem. 2010 May 1;82(9):3556-66 PMID: 20373789
  222. A single-stranded DNA aptamer that selectively binds to Staphylococcus aureus enterotoxin B.
    PLoS One. 2012;7(3):e33410 PMID: 22438927
  223. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
    Nat Biotechnol. 2004 Feb;22(2):177-83 PMID: 14755292
  224. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis.
    Curr Biol. 2010 May 25;20(10):951-6 PMID: 20409711
  225. PaxDb, a database of protein abundance averages across all three domains of life.
    Mol Cell Proteomics. 2012 Aug;11(8):492-500 PMID: 22535208
  226. Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: a novel method to determine interresidue distances in protein structures through cross-linking.
    J Proteome Res. 2010 Jul 2;9(7):3583-9 PMID: 20476776
  227. Role of intrinsic disorder in transient interactions of hub proteins.
    Proteins. 2007 Mar 1;66(4):761-5 PMID: 17154416
  228. SAINT: probabilistic scoring of affinity purification-mass spectrometry data.
    Nat Methods. 2011 Jan;8(1):70-3 PMID: 21131968
  229. Human cytomegalovirus elevates levels of the cellular protein p53 in infected fibroblasts.
    J Virol. 1994 Dec;68(12):8028-34 PMID: 7966592
  230. Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
    Mol Syst Biol. 2007;3:116 PMID: 17551511
  231. A generic protein purification method for protein complex characterization and proteome exploration.
    Nat Biotechnol. 1999 Oct;17(10):1030-2 PMID: 10504710
  232. Epitope tagging.
    Biotechniques. 2008 Apr;44(5):693-5 PMID: 18474046
  233. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.
    Nature. 2007 Apr 12;446(7137):806-10 PMID: 17314980
  234. Advances in preparation of biological extracts for protein purification.
    Methods Enzymol. 2009;463:285-303 PMID: 19892178
  235. The mzIdentML data standard for mass spectrometry-based proteomics results.
    Mol Cell Proteomics. 2012 Jul;11(7):M111.014381 PMID: 22375074
  236. An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network.
    Mol Cell Proteomics. 2006 Feb;5(2):366-78 PMID: 16284124
  237. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
    Nat Methods. 2012 Apr;9(4):345-50 PMID: 22453911
  238. Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.
    Mol Syst Biol. 2011 Nov 08;7:547 PMID: 22068330
  239. A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies.
    J Exp Bot. 2006;57(7):1501-8 PMID: 16574745
  240. Interactome study suggests multiple cellular functions of hepatoma-derived growth factor (HDGF).
    J Proteomics. 2011 Dec 21;75(2):588-602 PMID: 21907836
  241. Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication.
    J Virol. 2010 Jul;84(13):6720-32 PMID: 20392851
  242. A method for the rapid and efficient elution of native affinity-purified protein A tagged complexes.
    J Proteome Res. 2005 Nov-Dec;4(6):2250-6 PMID: 16335973
  243. Herpes simplex virus 1 ICP4 forms complexes with TFIID and mediator in virus-infected cells.
    J Virol. 2011 Jun;85(12):5733-44 PMID: 21450820
Article Info
Journal
Analytical chemistry
Abbr.
Anal Chem
ISSN
1520-6882
DOI
10.1021/ac3033257
Published
2013-01-15
Epub
2012-00-12
Pages
749-68
Language
English
Region
United States
NLM ID
0370536
PMCID
PMC3666915
Subset
IM
Grants
NIDA NIH HHS · DP1 DA026192 · United States
NIAID NIH HHS · R21 AI102187 · United States
NIAID NIH HHS · R21AI102187 · United States
NIDA NIH HHS · DP1DA026192 · United States
External Links
PubMed source DOI: 10.1021/ac3033257 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2