Mass spectrometry-based signal networks elucidation

Current Opinion in Biotechnology

Volumn 23, Issue 1, 2012, Pages 120-125

  He, Kun ^a   Wang, Na ^a   Li, Wei Hua ^a   Zhang, Xue Min ^a  

^a NATIONAL CENTER OF BIOMEDICAL ANALYSIS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION ANALYSIS; MOLECULAR PROPERTIES; POST-TRANSCRIPTIONAL MECHANISMS; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN COMPLEXES; PROTEIN EXPRESSIONS; PROTEOMICS; QUANTUM LEAPS; SIGNALLING NETWORK;

GENE EXPRESSION; MASS SPECTROMETRY; MOLECULAR BIOLOGY;

PROTEINS;

AMYLOID BETA PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MICRORNA; MICRORNA 17; MICRORNA 92; TAU PROTEIN; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG;

CELL FUNCTION; CELLULAR DISTRIBUTION; DYNAMICS; HIGH THROUGHPUT SCREENING; HUMAN; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DYNAMICS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STABILITY; REVIEW; SIGNAL TRANSDUCTION; SUMOYLATION; UBIQUITINATION;

ANIMALS; HUMANS; MASS SPECTROMETRY; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 84856480820     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.10.011     Document Type: Review

References (46)

1. Han X., Aslanian A., Yates J.R. Mass spectrometry for proteomics. Current Opinion in Chemical Biology 2008, 12:483-490.
2. Walther T.C., Mann M. Mass spectrometry-based proteomics in cell biology. The Journal of Cell Biology 2010, 190:491-500.
3. Choudhary C., Mann M. Decoding signalling networks by mass spectrometry-based proteomics. Nature Reviews Molecular Cell Biology 2010, 11:427-439.
4. Mann M. Functional and quantitative proteomics using SILAC. Nature Reviews Molecular Cell Biology 2006, 7:952-958.
5. Bartke T., Vermeulen M., Xhemalce B., Robson S.C., Mann M., Kouzarides T. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 2010, 143:470-484.
6. Forrester M.T., Thompson J.W., Foster M.W., Nogueira L., Moseley M.A., Stamler J.S. Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. Nature Biotechnology 2009, 27:557-559.
7. Rhein V., Song X., Wiesner A., Ittner L.M., Baysang G., Meier F., Ozmen L., Bluethmann H., Drose S., Brandt U., Savaskan E., et al. Amyloid-β and tau synergistically impair the oxidative phosphorylation system in triple transgenic Alzheimer's disease mice. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:20057-20062.
8. Cima I., Schiess R., Wild P., Kaelin M., Schuffler P., Lange V., Picotti P., Ossola R., Templeton A., Schubert O., Fuchs T., et al. Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:3342-3347.
9. Luber C.A., Cox J., Lauterbach H., Fancke B., Selbach M., Tschopp J., Akira S., Wiegand M., Hochrein H., O'Keeffe M. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32:279-289.
10. Mestdagh P., Boström A.-K., Impens F., Fredlund E., Van Peer G., De Antonellis P., von Stedingk K., Ghesquière B., Schulte S., Dews M., Thomas-Tikhonenko A., et al. The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma. Molecular Cell 2010, 40:762-773.
11. Boisvert F.M., Lam Y.W., Lamont D., Lamond A.I. A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Molecular & Cellular Proteomics 2009, 9:457-470.
12. Pagliarini D.J., Calvo S.E., Chang B., Sheth S.A., Vafai S.B., Ong S.-E., Walford G.A., Sugiana C., Boneh A., Chen W.K. A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008, 134:112-123.
13. Jakobsen L., Vanselow K., Skogs M., Toyoda Y., Lundberg E., Poser I., Falkenby L.G., Bennetzen M., Westendorf J., Nigg E.A., Uhlen M., et al. Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods. The EMBO Journal 2011, 30:1520-1535.
14. Lam Y.W., Evans V.C., Heesom K.J., Lamond A.I., Matthews D.A. Proteomics analysis of the nucleolus in adenovirus-infected cells. Molecular and Cellular Proteomics 2010, 9:117-130.
15. Ohta S., Bukowski-Wills J.-C., Sanchez-Pulido L., Alves FdL, Wood L., Chen Z.A., Platani M., Fischer L., Hudson D.F., Ponting C.P., Fukagawa T., et al. The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell 2010, 142:810-821.
16. Malmström J., Beck M., Schmidt A., Lange V., Deutsch E.W., Aebersold R. Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature 2009, 460:762-765.
17. Whiteaker J.R., Lin C., Kennedy J., Hou L., Trute M., Sokal I., Yan P., Schoenherr R.M., Zhao L., Voytovich U.J., Kelly-Spratt K.S., et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nature Biotechnology 2011, 29:625-634.
18. Picotti P., Bodenmiller B., Mueller L.N., Domon B., Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 2009, 138:795-806.
19. Kubota K., Anjum R., Yu Y., Kunz R.C., Andersen J.N., Kraus M., Keilhack H., Nagashima K., Krauss S., Paweletz C., Hendrickson R.C., et al. Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nature Biotechnology 2009, 27:933-940.
20. 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., et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Science Signaling 2010, 3:ra3.
21. Gao Y.-F., Li T., Chang Y., Wang Y.-B., Zhang W.-N., Li W.-H., He K., Mu R., Zhen C., Man J.-H., Pan X., et al. Cdk1-phosphorylated CUEDC2 promotes spindle checkpoint inactivation and chromosomal instability. Nature Cell Biology 2011, 13:924-933.
22. Man J., Zhang X. CUEDC2: an emerging key player in inflammation and tumorigenesis. Protein & Cell 2011, 2:699-703.
23. Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 2009, 325:1682-1686.
24. Fang M., Shen Z., Huang S., Zhao L., Chen S., Mak T.W., Wang X. The ER UDPase ENTPD5 promotes protein N-glycosylation, the Warburg Effect, and proliferation in the PTEN pathway. Cell 2010, 143:711-724.
25. Capotosti F., Guernier S., Lammers F., Waridel P., Cai Y., Jin J., Conaway J.W., Conaway R.C., Herr W. O-GlcNAc transferase catalyzes site-specific proteolysis of HCF-1. Cell 2011, 144:376-388.
26. Kim S.C., Sprung R., Chen Y., Xu Y., Ball H., Pei J., Cheng T., Kho Y., Xiao H., Xiao L., Grishin N.V., et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Molecular Cell 2006, 23:607-618.
27. Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009, 325:834-840.
28. Wang Q., Zhang Y., Yang C., Xiong H., Lin Y., Yao J., Li H., Xie L., Zhao W., Yao Y., Ning Z.B., et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 2010, 327:1004-1007.
29. Zhao S., Xu W., Jiang W., Yu W., Lin Y., Zhang T., Yao J., Zhou L., Zeng Y., Li H., Li Y., et al. Regulation of cellular metabolism by protein lysine acetylation. Science 2010, 327:1000-1004.
30. Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. A proteomics approach to understanding protein ubiquitination. Nature Biotechnology 2003, 21:921-926.
31. Ryu H., Furuta M., Kirkpatrick D., Gygi S.P., Azuma Y. PIASy-dependent SUMOylation regulates DNA topoisomerase II activity. The Journal of Cell Biology 2010, 191:783-794.
32. Xu G., Paige J.S., Jaffrey S.R. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nature Biotechnology 2010, 28:868-873.
33. Xu P., Duong D.M., Seyfried N.T., Cheng D., Xie Y., Robert J., Rush J., Hochstrasser M., Finley D., Peng J. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 2009, 137:133-145.
34. Tokunaga F., Sakata S., Saeki Y., Satomi Y., Kirisako T., Kamei K., Nakagawa T., Kato M., Murata S., Yamaoka S., Yamamoto M., et al. Involvement of linear polyubiquitylation of NEMO in NF-kappaB activation. Nature Cell Biology 2009, 11:123-132.
35. Gerlach B., Cordier S.M., Schmukle A.C., Emmerich C.H., Rieser E., Haas T.L., Webb A.I., Rickard J.A., Anderton H., Wong W.W.L., Nachbur U., et al. Linear ubiquitination prevents inflammation and regulates immune signalling. Nature 2011, 471:591-596.
36. Vermeulen M., Hubner N.C., Mann M. High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Current Opinion in Biotechnology 2008, 19:331-337.
37. van den Berg D.L.C., Snoek T., Mullin N.P., Yates A., Bezstarosti K., Demmers J., Chambers I., Poot R.A. An Oct4-centered protein interaction network in embryonic stem cells. Cell Stem Cell 2010, 6:369-381.
38. Bienvenu F., Jirawatnotai S., Elias J.E., Meyer C.A., Mizeracka K., Marson A., Frampton G.M., Cole M.F., Odom D.T., Odajima J., Geng Y., et al. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature 2010, 463:374-378.
39. Abramson J., Giraud M., Benoist C., Mathis D. Aire's partners in the molecular control of immunological tolerance. Cell 2010, 140:123-135.
40. Sang L., Miller Julie J., Corbit Kevin C., Giles Rachel H., Brauer Matthew J., Otto Edgar A., Baye Lisa M., Wen X., Scales Suzie J., Kwong M., Huntzicker Erik G., et al. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Cell 2011, 145:513-528.
41. MacKay C., Déclais A.-C., Lundin C., Agostinho A., Deans A.J., MacArtney T.J., Hofmann K., Gartner A., West S.C., Helleday T., Lilley D.M.J., et al. Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2. Cell 2010, 142:65-76.
42. Hutchins J.R.A., Toyoda Y., Hegemann B., Poser I., Heriche J.K., Sykora M.M., Augsburg M., Hudecz O., Buschhorn B.A., Bulkescher J., Conrad C., et al. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, 328:593-599.
43. Malovannaya A., Lanz Rainer B., Jung Sung Y., Bulynko Y., Le Nguyen T., Chan Doug W., Ding C., Shi Y., Yucer N., Krenciute G., Kim B.-J., et al. Analysis of the human endogenous coregulator complexome. Cell 2011, 145:787-799.
44. Bennett E.J., Rush J., Gygi S.P., Harper J.W. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 2010, 143:951-965.
45. Butter F., Scheibe M., Morl M., Mann M. Unbiased RNA-protein interaction screen by quantitative proteomics. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:10626-10631.
46. Vermeulen M., Eberl H.C., Matarese F., Marks H., Denissov S., Butter F., Lee K.K., Olsen J.V., Hyman A.A., Stunnenberg H.G., Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 2010, 142:967-980.