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References
42
Referenced
143
- Ito T, Tashiro K, Kuhara T Systematic analysis of Saccharomyces cerevisiae genome: gene network and protein-protein interaction network. Tanpakushitsu Kakusan Koso 46 2407–2413 2001 / Tanpakushitsu Kakusan Koso by T Ito (2001)
-
Uetz P, Hughes RE Systematic and large-scale two-hybrid screens. Curr. Opin. Microbiol. 3 303–308 2000
(
10.1016/S1369-5274(00)00094-1
) / Curr. Opin. Microbiol. by P Uetz (2000) -
Gavin AC et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 141–147 2002
(
10.1038/415141a
) / Nature by AC Gavin (2002) -
Gavin AC et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 631–636 2006
(
10.1038/nature04532
) / Nature by AC Gavin (2006) -
Ho Y et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 180–183 2002
(
10.1038/415180a
) / Nature by Y Ho (2002) -
Krogan NJ et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 637–643 2006
(
10.1038/nature04670
) / Nature by NJ Krogan (2006) -
Butland G et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531–537 2005
(
10.1038/nature03239
) / Nature by G Butland (2005) - Figeys D Functional proteomics: mapping protein-protein interactions and pathways. Curr. Opin. Mol. Ther. 4 210–215 2002 / Curr. Opin. Mol. Ther. by D Figeys (2002)
-
Verma R et al. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11 3425–3439 2000
(
10.1091/mbc.11.10.3425
) / Mol. Biol. Cell by R Verma (2000) -
Gygi SP et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 994–999 1999
(
10.1038/13690
) / Nat. Biotechnol. by SP Gygi (1999) -
Ross PL et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3 1154–1169 2004
(
10.1074/mcp.M400129-MCP200
) / Mol. Cell. Proteomics by PL Ross (2004) -
Schmidt A, Kellermann J, Lottspeich F A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5 4–15 2005
(
10.1002/pmic.200400873
) / Proteomics by A Schmidt (2005) -
Ong SE et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1 376–386 2002
(
10.1074/mcp.M200025-MCP200
) / Mol. Cell. Proteomics by SE Ong (2002) -
Oda Y, Huang K, Cross FR, Cowburn D, Chait BT Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 96 6591–6596 1999
(
10.1073/pnas.96.12.6591
) / Proc. Natl. Acad. Sci. USA by Y Oda (1999) -
Ranish JA et al. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33 349–355 2003
(
10.1038/ng1101
) / Nat. Genet. by JA Ranish (2003) -
Himeda CL et al. Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer. Mol. Cell. Biol. 24 2132–2143 2004
(
10.1128/MCB.24.5.2132-2143.2004
) / Mol. Cell. Biol. by CL Himeda (2004) -
Blagoev B et al. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 21 315–318 2003
(
10.1038/nbt790
) / Nat. Biotechnol. by B Blagoev (2003) -
Brand M et al. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat. Struct. Mol. Biol. 11 73–80 2004
(
10.1038/nsmb713
) / Nat. Struct. Mol. Biol. by M Brand (2004) -
Li XJ, Yi EC, Kemp CJ, Zhang H, Aebersold R A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 4 1328–1340 2005
(
10.1074/mcp.M500141-MCP200
) / Mol. Cell. Proteomics by XJ Li (2005) -
Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ Absolute quantification of proteins by LCMS: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 5 144–156 2006
(
10.1074/mcp.M500230-MCP200
) / Mol. Cell. Proteomics by JC Silva (2006) -
Callister SJ et al. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J. Proteome Res. 5 277–286 2006
(
10.1021/pr050300l
) / J. Proteome Res. by SJ Callister (2006) -
Andersen JS et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426 570–574 2003
(
10.1038/nature02166
) / Nature by JS Andersen (2003) -
Brunet A et al. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science 303 2011–2015 2004
(
10.1126/science.1094637
) / Science by A Brunet (2004) -
Keller A, Nesvizhskii AI, Kolker E, Aebersold R Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74 5383–5392 2002
(
10.1021/ac025747h
) / Anal. Chem. by A Keller (2002) -
Van Der Heide LP, Hoekman MF, Smidt MP The ins and outs of FoxO shuttling: mechanisms of FoxO translocation and transcriptional regulation. Biochem. J. 380 297–309 2004
(
10.1042/bj20040167
) / Biochem. J. by LP Van Der Heide (2004) -
Brunet A et al. Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor. Cell 96 857–868 1999
(
10.1016/S0092-8674(00)80595-4
) / Cell by A Brunet (1999) -
Brunet A et al. 14–3-3 transits to the nucleus and participates in dynamic nucleocytoplasmic transport. J. Cell Biol. 156 817–828 2002
(
10.1083/jcb.200112059
) / J. Cell Biol. by A Brunet (2002) -
Nesvizhskii AI, Keller A, Kolker E, Aebersold R A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75 4646–4658 2003
(
10.1021/ac0341261
) / Anal. Chem. by AI Nesvizhskii (2003) -
Nesvizhskii AI, Aebersold R Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4 1419–1440 2005
(
10.1074/mcp.R500012-MCP200
) / Mol. Cell. Proteomics by AI Nesvizhskii (2005) -
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20 3551–3567 1999
(
10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
) / Electrophoresis by DN Perkins (1999) -
Kops GJ et al. Direct control of the Forkhead transcription factor AFX by protein kinase B. Nature 398 630–634 1999
(
10.1038/19328
) / Nature by GJ Kops (1999) -
Liu H, Sadygov RG, Yates JR III A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76 4193–4201 2004
(
10.1021/ac0498563
) / Anal. Chem. by H Liu (2004) -
Gavin IM, Kukhtin A, Glesne D, Schabacker D, Chandler DP Analysis of protein interaction and function with a 3-dimensional MALDI-MS protein array. Biotechniques 39 99–107 2005
(
10.2144/05391RR02
) / Biotechniques by IM Gavin (2005) -
Guerrero C, Tagwerker C, Kaiser P, Huang L An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26S proteasome-interacting network. Mol. Cell. Proteomics 5 366–378 2006
(
10.1074/mcp.M500303-MCP200
) / Mol. Cell. Proteomics by C Guerrero (2006) -
Smith RD et al. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2 513–523 2002
(
10.1002/1615-9861(200205)2:5<513::AID-PROT513>3.0.CO;2-W
) / Proteomics by RD Smith (2002) -
Chen SS, Aebersold R LC-MS solvent composition monitoring and chromatography alignment using mobile phase tracer molecules. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 829 107–114 2005
(
10.1016/j.jchromb.2005.09.039
) / J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. by SS Chen (2005) - Duda RO, Hart PE, Stork DG Pattern Classification vol. 1, edn. 2, (Wiley-Interscience, New York, 2000) / Pattern Classification by RO Duda (2000)
-
Nesvizhskii AI, Aebersold R Analysis, statistical validation and dissemination of large-scale proteomics data sets generated by tandem MS. Drug Discov. Today 9 173–181 2004
(
10.1016/S1359-6446(03)02978-7
) / Drug Discov. Today by AI Nesvizhskii (2004) -
Hastie T, Tibshirani R, Friedman J The Elements of Statistical Learning (Springer, New York, 2001)
(
10.1007/978-0-387-21606-5
) / The Elements of Statistical Learning by T Hastie (2001) -
Colinge J, Masselot A, Carbonell P, Appel RD InSilicoSpectro: an open-source proteomics library. J. Proteome Res. 5 619–624 2006
(
10.1021/pr0504236
) / J. Proteome Res. by J Colinge (2006) -
Keller A, Eng J, Zhang N, Li XJ, Aebersold R A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 1 2005, 0017 2005
(
10.1038/msb4100024
) / Mol. Syst. Biol. by A Keller (2005) -
Shannon P et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 2498–2504 2003
(
10.1101/gr.1239303
) / Genome Res. by P Shannon (2003)
Dates
Type | When |
---|---|
Created | 18 years, 6 months ago (Feb. 25, 2007, 12:56 p.m.) |
Deposited | 2 years, 3 months ago (May 18, 2023, 3:51 p.m.) |
Indexed | 1 year ago (Aug. 4, 2024, 1:11 a.m.) |
Issued | 18 years, 6 months ago (Feb. 25, 2007) |
Published | 18 years, 6 months ago (Feb. 25, 2007) |
Published Online | 18 years, 6 months ago (Feb. 25, 2007) |
Published Print | 18 years, 5 months ago (March 1, 2007) |
@article{Rinner_2007, title={An integrated mass spectrometric and computational framework for the analysis of protein interaction networks}, volume={25}, ISSN={1546-1696}, url={http://dx.doi.org/10.1038/nbt1289}, DOI={10.1038/nbt1289}, number={3}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Rinner, Oliver and Mueller, Lukas N. and Hubálek, Martin and Müller, Markus and Gstaiger, Matthias and Aebersold, Ruedi}, year={2007}, month=feb, pages={345–352} }