Proteomics methods for subcellular proteome analysis

FEBS Journal

Volumn 280, Issue 22, 2013, Pages 5626-5634

  Drissi, Romain ^a   Dubois, Marie Line ^a   Boisvert, François Michel ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

MS; organelle; proteomics; stable isotope labeling by amino acids in cell culture (SILAC); subcellular compartment

Indexed keywords

PROTEOME;

ARTICLE; BIOINFORMATICS; CELL ORGANELLE; CELLULAR DISTRIBUTION; MASS SPECTROMETRY; MOLECULAR DYNAMICS; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEOMICS; QUANTITATIVE STUDY;

MS; ORGANELLE; PROTEOMICS; STABLE ISOTOPE LABELING BY AMINO ACIDS IN CELL CULTURE (SILAC); SUBCELLULAR COMPARTMENT;

CELL FRACTIONATION; CELL LINE; COMPUTATIONAL BIOLOGY; HUMANS; MASS SPECTROMETRY; ORGANELLES; PROTEOME; PROTEOMICS; SUBCELLULAR FRACTIONS;

EID: 84886583029     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12502     Document Type: Article

References (52)

1. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, &, Lamond AI, (2002) Directed proteomic analysis of the human nucleolus. Curr Biol 12, 1-11.
2. Andersen JS, &, Mann M, (2006) Organellar proteomics: turning inventories into insights. EMBO Rep 7, 874-879.
3. Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Gosline SJ, Hallett M, et al,. (2006) Quantitative proteomics analysis of the secretory pathway. Cell 127, 1265-1281.
4. Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, et al,. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125, 173-186.
5. Wiese S, Gronemeyer T, Ofman R, Kunze M, Grou CP, Almeida JA, Eisenacher M, Stephan C, Hayen H, Schollenberger L, et al,. (2007) Proteomics characterization of mouse kidney peroxisomes by tandem mass spectrometry and protein correlation profiling. Mol Cell Proteomics 6, 2045-2057.
6. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, &, Mann M, (2006) A mammalian organelle map by protein correlation profiling. Cell 125, 187-199.
7. Dunkley TP, Watson R, Griffin JL, Dupree P, &, Lilley KS, (2004) Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3, 1128-1134.
8. Sadowski PG, Dunkley TP, Shadforth IP, Dupree P, Bessant C, Griffin JL, &, Lilley KS, (2006) Quantitative proteomic approach to study subcellular localization of membrane proteins. Nat Protoc 1, 1778-1789.
9. Gauthier DJ, &, Lazure C, (2008) Complementary methods to assist subcellular fractionation in organellar proteomics. Expert Rev Proteomics 5, 603-617.
10. Hall SL, Hester S, Griffin JL, Lilley KS, &, Jackson AP, (2009) The organelle proteome of the DT40 lymphocyte cell line. Mol Cell Proteomics 8, 1295-1305.
11. Walther TC, &, Mann M, (2010) Mass spectrometry-based proteomics in cell biology. J Cell Biol 190, 491-500.
12. Takatalo MS, Kouvonen P, Corthals G, Nyman TA, &, Ronnholm RH, (2006) Identification of new Golgi complex specific proteins by direct organelle proteomic analysis. Proteomics 6, 3502-3508.
13. Noble WS, &, MacCoss MJ, (2012) Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol 8, e1002296.
14. Taylor SW, Fahy E, Zhang B, Glenn GM, Warnock DE, Wiley S, Murphy AN, Gaucher SP, Capaldi RA, Gibson BW, et al. (2003) Characterization of the human heart mitochondrial proteome. Nat Biotechnol 21, 281-286.
15. Ramsby ML, Makowski GS, &, Khairallah EA, (1994) Differential detergent fractionation of isolated hepatocytes: biochemical, immunochemical and two-dimensional gel electrophoresis characterization of cytoskeletal and noncytoskeletal compartments. Electrophoresis 15, 265-277.
16. Sawhney S, Stubbs R, &, Hood K, (2009) Reproducibility, sensitivity and compatibility of the ProteoExtract subcellular fractionation kit with saturation labeling of laser microdissected tissues. Proteomics 9, 4087-4092.
17. Hannig K, &, Wrba H, (1964) [Isolation of vital tumor cells by carrier-free electrophoresis]. Z Naturforsch B 19, 860.
18. Volkl A, Mohr H, Weber G, &, Fahimi HD, (1997) Isolation of rat hepatic peroxisomes by means of immune free flow electrophoresis. Electrophoresis 18, 774-780.
19. Tulp A, Verwoerd D, Benham A, &, Neefjes J, (1997) High-resolution density gradient electrophoresis of proteins and subcellular organelles. Electrophoresis 18, 2509-2515.
20. Bauer A, &, Kuster B, (2003) Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes. Eur J Biochem 270, 570-578.
21. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, et al,. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
22. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al,. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
23. Yates JR 3rd, Gilchrist A, Howell KE, &, Bergeron JJ, (2005) Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 6, 702-714.
24. Bell AW, Ward MA, Blackstock WP, Freeman HN, Choudhary JS, Lewis AP, Chotai D, Fazel A, Gushue JN, Paiement J, et al,. (2001) Proteomics characterization of abundant Golgi membrane proteins. J Biol Chem 276, 5152-5165.
25. Wasiak S, Legendre-Guillemin V, Puertollano R, Blondeau F, Girard M, de Heuvel E, Boismenu D, Bell AW, Bonifacino JS, &, McPherson PS, (2002) Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics. J Cell Biol 158, 855-862.
26. Scharfe C, Zaccaria P, Hoertnagel K, Jaksch M, Klopstock T, Lill R, Prokisch H, Gerbitz KD, Mewes HW, &, Meitinger T, (1999) MITOP: database for mitochondria-related proteins, genes and diseases. Nucleic Acids Res 27, 153-155.
27. Garin J, Diez R, Kieffer S, Dermine JF, Duclos S, Gagnon E, Sadoul R, Rondeau C, &, Desjardins M, (2001) The phagosome proteome: insight into phagosome functions. J Cell Biol 152, 165-180.
28. Dreger M, Bengtsson L, Schoneberg T, Otto H, &, Hucho F, (2001) Nuclear envelope proteomics: novel integral membrane proteins of the inner nuclear membrane. Proc Natl Acad Sci USA 98, 11943-11948.
29. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, &, Chait BT, (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148, 635-651.
30. Neubauer G, Gottschalk A, Fabrizio P, Seraphin B, Luhrmann R, &, Mann M, (1997) Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci USA 94, 385-390.
31. Wu CC, MacCoss MJ, Howell KE, &, Yates JR 3rd, (2003) A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 21, 532-538.
32. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, &, Mann M, (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574.
33. Krahmer N, Hilger M, Kory N, Wilfling F, Stoehr G, Mann M, Farese RV Jr, &, Walther TC, (2013) Protein correlation profiles identify lipid droplet proteins with high confidence. Mol Cell Proteomics 12, 1115-1126.
34. Steen H, &, Mann M, (2004) The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5, 699-711.
35. Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, &, Aebersold R, (2011) The quantitative proteome of a human cell line. Mol Syst Biol 7, 549.
36. Leung AK, Andersen JS, Mann M, &, Lamond AI, (2003) Bioinformatic analysis of the nucleolus. Biochem J 376, 553-569.
37. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, &, Mann M, (2005) Nucleolar proteome dynamics. Nature 433, 77-83.
38. Ahmad Y, Boisvert FM, Gregor P, Cobley A, &, Lamond AI, (2009) NOPdb: Nucleolar Proteome Database-2008 update. Nucleic Acids Res 37, D181-D184.
39. Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez AriasA, &, Lilley KS, (2009) Mapping organelle proteins and protein complexes in Drosophila melanogaster. J Proteome Res 8, 2667-2678.
40. Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, et al,. (2006) Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci USA 103, 6518-6523.
41. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, &, Mann M, (2002) 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.
42. Boisvert FM, Lam YW, Lamont D, &, Lamond AI, (2010) A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Mol Cell Proteomics 9, 457-470.
43. Lamond AI, Uhlen M, Horning S, Makarov A, Robinson CV, Serrano L, Hartl FU, Baumeister W, Werenskiold AK, Andersen JS, et al,. (2012) Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics 11, O112-O017731.
44. Chappell NP, Teng PN, Hood BL, Wang G, Darcy KM, Hamilton CA, Maxwell GL, &, Conrads TP, (2012) Mitochondrial proteomic analysis of cisplatin resistance in ovarian cancer. J Proteome Res 11, 4605-4614.
45. Boisvert FM, &, Lamond AI, (2010) p53-Dependent subcellular proteome localization following DNA damage. Proteomics 10, 4087-4097.
46. Larance M, Ahmad Y, Kirkwood KJ, Ly T, &, Lamond AI, (2013) Global subcellular characterization of protein degradation using quantitative proteomics. Mol Cell Proteomics 12, 638-650.
47. Schwanhausser B, Gossen M, Dittmar G, &, Selbach M, (2009) Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9, 205-209.
48. Boisvert FM, Ahmad Y, Gierlinski M, Charriere F, Lamont D, Scott M, Barton G, &, Lamond AI, (2012) A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol Cell Proteomics 11, M111-M011429.
49. Savas JN, Toyama BH, Xu T, Yates JR 3rd, &, Hetzer MW, (2012) Extremely long-lived nuclear pore proteins in the rat brain. Science 335, 942.
50. Donnes P, &, Hoglund A, (2004) Predicting protein subcellular localization: past, present, and future. Genomics Proteomics Bioinformatics 2, 209-215.
51. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al,. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29.
52. Trotter MW, Sadowski PG, Dunkley TP, Groen AJ, &, Lilley KS, (2010) Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 10, 4213-4219.