Mapping and analysis of phosphorylation sites: A quick guide for cell biologists

Molecular Biology of the Cell

Volumn 24, Issue 5, 2013, Pages 535-542

  Dephoure, Noah ^a   Gould, Kathleen L ^b   Gygi, Steven P ^a   Kellogg, Douglas R ^c  

^a HARVARD MEDICAL SCHOOL   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOAMINO ACID; PHOSPHOPEPTIDE; PROTEOME;

HYDROPHOBICITY; IONIZATION; MASS SPECTROMETRY; MICROBIOLOGY; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEOMICS; REVIEW; STOICHIOMETRY;

AMINO ACID SEQUENCE; AMINO ACIDS; CHROMOSOME MAPPING; DATABASES, PROTEIN; PEPTIDE FRAGMENTS; PHOSPHOPROTEINS; PHOSPHORYLATION; SIGNAL TRANSDUCTION; TANDEM MASS SPECTROMETRY;

EID: 84874589189     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E12-09-0677     Document Type: Review

References (54)

1. Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP (2006). A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24, 1285-1292. (Pubitemid 44564776)
2. Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ (2009). Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc 4, 484-494.
3. Boyle WJ, van der Geer P, Hunter T (1991). Phosphopeptide mapping and phosphoamino acid analysis by two-dimensional separation on thin-layer cellulose plates. Methods Enzymol 201, 110-149.
4. Choi KY, Satterberg B, Lyons DM, Elion EA (1994). Ste5 tethers multiple protein kinases in the MAP kinase cascade required for mating in S. cerevisiae. Cell 78, 499-512. (Pubitemid 24250813)
5. Cooper JA, Sefton BM, Hunter T (1984). Diverse mitogenic agents induce the phosphorylation of two related 42,000-dalton proteins on tyrosine in quiescent chick cells. Mol Cell Biol 4, 30-37.
6. Craig R, Beavis RC (2004). TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467. (Pubitemid 38931421)
7. Dard N, Peter M (2006). Scaffold proteins in MAP kinase signaling: more than simple passive activating platforms. BioEssays 28, 146-156.
8. Den Haese GJ, Walworth N, Carr AM, Gould KL (1995). The Wee1 protein kinase regulates T14 phosphorylation of fission yeast Cdc2. Mol Biol Cell 6, 371-385.
9. Dinkel H et al. (2012). ELM -the database of eukaryotic linear motifs. Nucl Acids Res 40, D242-D251.
10. Durocher D, Henckel J, Fersht AR, Jackson SP (1999). The FHA domain is a modular phosphopeptide recognition motif. Mol Cell 4, 387-394. (Pubitemid 29499791)
11. Elias JE, Gygi SP (2007). Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4, 207-214. (Pubitemid 46358868)
12. Eng JK, McCormack AL, Yates J 3rd (1994). An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Spectrom 5, 976-989.
13. Fenyo D, Beavis RC (2003). A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem 75, 768-774. (Pubitemid 36232428)
14. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004). Open mass spectrometry search algorithm. J Proteome Res 3, 958-964. (Pubitemid 39425651)
15. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003). Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100, 6940-6945. (Pubitemid 36706372)
16. Gingras AC, Gstaiger M, Raught B, Aebersold R (2007). Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8, 645-654. (Pubitemid 47106612)
17. Gsponer J, Futschik ME, Teichmann SA, Babu MM (2008). Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322, 1365-1368. (Pubitemid 352775246)
18. Harvey SL, Charlet A, Haas W, Gygi SP, Kellogg DR (2005). Cdk1-dependent regulation of the mitotic inhibitor Wee1. Cell 122, 407-420. (Pubitemid 41127142)
19. Harvey SL, Enciso G, Dephoure NE, Gygi SP, Gunawardena J, Kellogg DR (2011). A phosphatase threshold sets the level of Cdk1 activity in early mitosis. Mol Biol Cell 22, 3595-3608.
20. Ho Y et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183. (Pubitemid 34059520)
21. Hunter T (2012). Why nature chose phosphate to modify proteins. Phil Trans R Soc Lond B Biol Sci 367, 2513-2516.
22. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK (2004). The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32, 1037-1049. (Pubitemid 38854704)
23. Kamps MP, Sefton BM (1989). Acid and base hydrolysis of phosphoproteins bound to immobilon facilitates analysis of phosphoamino acids in gel-fractionated proteins. Anal Biochem 176, 22-27. (Pubitemid 19047023)
24. Kinoshita E, Kinoshita-Kikuta E, Koike T (2012). Phos-tag SDS-PAGE systems for phosphorylation profiling of proteins with a wide range of molecular masses under neutral pH conditions. Proteomics 12, 192-202.
25. Kinoshita E, Kinoshita-Kikuta E, Takiyama K, Koike T (2006). Phosphate-binding tag, a new tool to visualize phosphorylated proteins. Mol Cell Proteomics 5, 749-757.
26. Landry CR, Levy ED, Michnick SW (2009). Weak functional constraints on phosphoproteomes. Trends Genet 25, 193-197.
27. Ma H, McLean JR, Chao LF, Mana-Capelli S, Paramasivam M, Hagstrom KA, Gould KL, McCollum D (2012). A highly efficient multifunctional tandem affinity purification approach applicable to diverse organisms. Mol Cell Proteomics 11, 501-511.
28. McKay MM, Morrison DK (2007). Integrating signals from RTKs to ERK/MAPK. Oncogene 26, 3113-3121. (Pubitemid 46763008)
29. Miller ML et al. (2008). Linear motif atlas for phosphorylation-dependent signaling. Science Signal 1, ra2.
30. Mortensen E, McDonald H, Yates J, Kellogg DR (2002). Cell cycle-dependent assembly of a Gin4-septin complex. Mol Biol Cell 13, 2091-2105. (Pubitemid 34651495)
31. Nishiwaki T, Satomi Y, Kitayama Y, Terauchi K, Kiyohara R, Takao T, Kondo T (2007). A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria. EMBO J 26, 4029-4037. (Pubitemid 47367500)
32. Niu S, Wang Z, Ge D, Zhang G, Li Y (2012). Prediction of functional phosphorylation sites by incorporating evolutionary information. Protein Cell 3, 675-690.
33. Obenauer JC, Cantley LC, Yaffe MB (2003). Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31, 3635-3641. (Pubitemid 37442212)
34. Olsen JV et al. (2010). Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 3, ra3.
35. 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.
36. Pearlman SM, Serber Z, Ferrell JE Jr. (2011). A mechanism for the evolution of phosphorylation sites. Cell 147, 934-946.
37. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999). Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567. (Pubitemid 30007252)
38. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999). A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17, 1030-1032. (Pubitemid 29474865)
39. Roberts-Galbraith RH, Ohi MD, Ballif BA, Chen JS, McLeod I, McDonald WH, Gygi SP, Yates JR 3rd, Gould KL (2010). Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site. Mol Cell 39, 86-99.
40. Ross PL et al. (2004). Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3, 1154-1169.
41. Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, Cantley LC (1994). Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4, 973-982. (Pubitemid 124001033)
42. Steen H, Mann M (2004). The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5, 699-711. (Pubitemid 39208180)
43. Stemmann O, Zou H, Gerber SA, Gygi SP, Kirschner MW (2001). Dual inhibition of sister chromatid separation at metaphase. Cell 107, 715-726. (Pubitemid 34033665)
44. Strickfaden SC, Winters MJ, Ben-Ari G, Lamson RE, Tyers M, Pryciak PM (2007). A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell 128, 519-531. (Pubitemid 46198890)
45. Tabb DL, Fernando CG, Chambers MC (2007). MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeo-metric analysis. J Proteome Res 6, 654-661. (Pubitemid 46340169)
46. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (2003). Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75, 1895-1904. (Pubitemid 36438013)
47. van der Geer P, Pawson T (1995). The PTB domain: a new protein module implicated in signal transduction. Trends Biochem Sci 20, 277-280.
48. Walther TC, Mann M (2010). Mass spectrometry-based proteomics in cell biology. J Cell Biol 190, 491-500.
49. Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP (2011). A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods 8, 677-683.
50. Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC (2001). A motif-based profile scanning approach for genome-wide prediction of signal-ing pathways. Nat Biotechnol 19, 348-353. (Pubitemid 32275344)
51. Yaffe MB, Rittinger K, Volinia S, Caron PR, Aitken A, Leffers H, Gamblin SJ, Smerdon SJ, Cantley LC (1997). The structural basis for 14-3-3: phosphopeptide binding specificity. Cell 91, 961-971. (Pubitemid 28027829)
52. Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ (2002a). Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J Biol Chem 277, 39379-39387. (Pubitemid 35190911)
53. Zhang X, Jin QK, Carr SA, Annan RS (2002b). N-terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry. Rapid Commun Mass Spectrom 16, 2325-2332. (Pubitemid 36014712)
54. Zisch AH, Pazzagli C, Freeman AL, Schneller M, Hadman M, Smith JW, Ruoslahti E, Pasquale EB (2000). Replacing two conserved tyrosines of the EphB2 receptor with glutamic acid prevents binding of SH2 domains without abrogating kinase activity and biological responses. Oncogene 19, 177-187. (Pubitemid 30077213)