A perspective on proteomics in cell biology

Trends in Cell Biology

Volumn 24, Issue 4, 2014, Pages 257-264

  Ahmad, Yasmeen ^a   Lamond, Angus I ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; PROTEOME; PROTEIN;

CYTOLOGY; GENOME; HUMAN; ISOTOPE LABELING; MASS SPECTROMETRY; MEDICAL SOCIETY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN METABOLISM; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; ANIMAL; BIOLOGY; METABOLISM; PROCEDURES;

ANIMALS; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; MASS SPECTROMETRY; PROTEINS; PROTEOMICS;

EID: 84897099344     PISSN: 09628924     EISSN: 18793088     Source Type: Journal    
DOI: 10.1016/j.tcb.2013.10.010     Document Type: Review

References (44)

1. Lamond A.I., Mann M. Cell biology and the genome projects a concerted strategy for characterizing multiprotein complexes by using mass spectrometry. Trends Cell Biol. 1997, 7:139-142.
2. Eng J., et al. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
3. Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
4. Perkins D.N., et al. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
5. Cox J., et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10:1794-1805.
6. Moorhead G.B., et al. Emerging roles of nuclear protein phosphatases. Nat. Rev. Mol. Cell Biol. 2007, 8:234-244.
7. Maier T., et al. Correlation of mRNA and protein in complex biological samples. FEBS Lett. 2009, 583:3966-3973.
8. Andersen J.S., et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 2002, 12:1-11.
9. Andersen J.S., et al. Nucleolar proteome dynamics. Nature 2005, 433:77-83.
10. McClatchy D.B., et al. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res. 2007, 17:1378-1388.
11. Boisvert F-M., et al. A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol. Cell. Proteomics 2012, 11. M111.011429.
12. Boulon S., et al. Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol. Cell. Proteomics 2010, 9:861-879.
13. Larance M., et al. Global subcellular characterization of protein degradation using quantitative proteomics. Mol. Cell. Proteomics 2013, 12:638-650.
14. Trinkle-Mulcahy L., et al. Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J. Cell Biol. 2006, 172:679-692.
15. Oda Y., et al. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:6591-6596.
16. Lahm H.W., Langen H. Mass spectrometry: a tool for the identification of proteins separated by gels. Electrophoresis 2000, 21:2105-2114.
17. Ong S-E., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1:376-386.
18. Mann M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 2006, 7:952-958.
19. Kirchner M., Selbach M. In vivo quantitative proteome profiling: planning and evaluation of SILAC experiments. Methods Mol. Biol. 2012, 893:175-199.
20. Wu C.C., et al. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 2004, 76:4951-4959.
21. Gygi S.P., et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17:994-999.
22. Ross P.L., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3:1154-1169.
23. Thompson A., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75:1895-1904.
24. Everley R.A., et al. Increasing throughput in targeted proteomics assays: 54-plex quantitation in a single mass spectrometry run. Anal. Chem. 2013, 85:5340-5346.
25. Hebert A.S., et al. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat. Methods 2013, 10:332-334.
26. Wolters D.A., et al. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 2001, 73:5683-5690.
27. Washburn M.P., et al. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19:242-247.
28. Trinkle-Mulcahy L., et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 2008, 183:223-239.
29. Wheaton R.M., Bauman W.C. Non-ionic separations with ion exchange resins. Ann. N. Y. Acad. Sci. 1953, 57:159-176.
30. Olinares P.D., et al. Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering. Mol. Cell. Proteomics 2010, 9:1594-1615.
31. Havugimana P.C., et al. A census of human soluble protein complexes. Cell 2012, 150:1068-1081.
32. Kristensen A.R., et al. A high-throughput approach for measuring temporal changes in the interactome. Nat. Methods 2012, 9:907-909.
33. Kirkwood K.J., et al. characterisation of native protein complexes and protein isoform variation using size-fractionation based quantitative proteomics. Mol. Cell. Proteomics 2013, 10.1074/mcp.M113.032367.
34. Gnad F., et al. PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 2011, 39:D253-D260.
35. Szklarczyk D., et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2010, 39:D561-D568.
36. Da Wei H., et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2008, 4:44-57.
37. Uhlen M., et al. Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol. 2010, 28:1248-1250.
38. Vizcaino J.A., et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41:D1063-D1069.
39. Zeiler M., et al. A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol. Cell. Proteomics 2012, 11. O111.009613.
40. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9:555-566.
41. Beynon R.J., et al. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2005, 2:587-589.
42. Gerber S.A., et al. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:6940-6945.
43. Mann M., et al. The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 2013, 49:583-590.
44. Marcoux J., Robinson C.V. Twenty years of gas phase structural biology. Structure 2013, 21:1541-1550.