SILAC-based temporal phosphoproteomics

Methods in Molecular Biology

Volumn 1188, Issue , 2014, Pages 125-148

  Francavilla, Chiara ^a   Hekmat, Omid ^a   Blagoev, Blagoy ^b   Olsen, Jesper V ^a  

^a University of Copenhagen   (Denmark)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

In solution digestion; Orbitrap; Peptide enrichment; Phosphorylation; Phosphotyrosine; Q Exactive; SCX

Indexed keywords

AMINO ACID; STABLE ISOTOPE; TITANIUM DIOXIDE; TYROSINE; INORGANIC SALT; PHOSPHOPEPTIDE; PHOSPHOPROTEIN;

ANTIBODY AFFINITY; ARTICLE; CATION EXCHANGE; CELL CULTURE; CELL LYSATE; CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEOMICS; TANDEM MASS SPECTROMETRY; ANALYSIS; CHEMISTRY; HUMAN; ION EXCHANGE CHROMATOGRAPHY; ISOLATION AND PURIFICATION; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; PROCEDURES; PROTEIN DEGRADATION; SPATIOTEMPORAL ANALYSIS;

AMINO ACIDS; ANALYTIC SAMPLE PREPARATION METHODS; CELLS, CULTURED; CHROMATOGRAPHY, ION EXCHANGE; CHROMATOGRAPHY, LIQUID; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; PHOSPHOPEPTIDES; PHOSPHOPROTEINS; PROTEOLYSIS; PROTEOMICS; SALTS; SPATIO-TEMPORAL ANALYSIS;

EID: 84925883548     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1142-4_10     Document Type: Article

References (40)

1. Schlessinger J (2000) Cell signaling by receptor tyrosine kinases. Cell 103(2):211-225
2. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5): 646-674
3. Cohen P (2001) The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur J Biochem 268(19):5001-5010
4. Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 11(6): 427-439
5. Rigbolt KT, Blagoev B (2012) Quantitative phosphoproteomics to characterize signaling networks. Semin Cell Dev Biol 23(8):863-871
6. Dengjel J, Kratchmarova I, Blagoev B (2009) Receptor tyrosine kinase signaling: a view from quantitative proteomics. Mol Biosyst 5(10): 1112-1121
7. Luber CA, Cox J, Lauterbach H et al (2010) Quantitative proteomics reveals subset-specifi c viral recognition in dendritic cells. Immunity 32(2):279-289
8. Ong SE, Mann M (2006) A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 1(6):2650-2660
9. Ow SY, Salim M, Noirel J et al (2009) iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly". J Proteome Res 8(11):5347-5355
10. Boersema PJ, Foong LY, Ding VM et al (2010) In-depth qualitative and quantitative profi ling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffi nity purifi-cation and stable isotope dimethyl labeling. Mol Cell Proteomics 9(1):84-99
11. Ong SE, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376-386
12. Olsen JV, Blagoev B, Gnad F et al (2006) Global, in vivo, and site-specifi c phosphorylation dynamics in signaling networks. Cell 127(3):635-648
13. Rigbolt KT, Prokhorova TA, Akimov V et al (2011) System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal 4(164):rs3
14. Rikova K, Guo A, Zeng Q et al (2007) Global survey of phosphotyrosine signaling identifi es oncogenic kinases in lung cancer. Cell 131(6): 1190-1203
15. Matsuoka S, Ballif BA, Smogorzewska A et al (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316(5828):1160-1166
16. Nuhse TS, Stensballe A, Jensen ON et al (2003) Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affi nity chromatography and mass spectrometry. Mol Cell Proteomics 2(11): 1234-1243
17. Andersson L, Porath J (1986) Isolation of phosphoproteins by immobilized metal (Fe3+) affi nity chromatography. Anal Biochem 154(1): 250-254
18. Larsen MR, Thingholm TE, Jensen ON et al (2005) Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 4(7):873-886
19. Olsen JV, Macek B (2009) High accuracy mass spectrometry in large-scale analysis of protein phosphorylation. Methods Mol Biol 492: 131-142
20. Choudhary C, Kumar C, Gnad F et al (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325(5942):834-840
21. Hunter T (2009) Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol 21(2):140-146
22. Blagoev B, Ong SE, Kratchmarova I et al (2004) Temporal analysis of phosphotyrosinedependent signaling networks by quantitative proteomics. Nat Biotechnol 22(9):1139-1145
23. Zarei M, Sprenger A, Metzger F et al (2011) Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches. J Proteome Res 10(8): 3474-3483
24. Olsen JV, Schwartz JC, Griep-Raming J et al (2009) A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 8(12):2759-2769
25. Kelstrup CD, Young C, Lavallee R et al (2012) Optimized fast and sensitive acquisition methods for shotgun proteomics on a Quadrupole Orbitrap mass spectrometer. J Proteome Res 11(6):3487-3497
26. Michalski A, Damoc E, Hauschild JP et al (2011) Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10(9):M111.011015
27. Cox J, Mann M (2008) MaxQuant enables high peptide identifi cation rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantifi cation. Nat Biotechnol 26(12):1367-1372
28. Cox J, Matic I, Hilger M et al (2009) A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc 4(5):698-705
29. Cox J, Neuhauser N, Michalski A et al (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10(4):1794-1805
30. Olsen JV, Macek B, Lange O et al (2007) Higher-energy C-trap dissociation for peptide modifi cation analysis. Nat Methods 4(9): 709-712
31. Nagaraj N, D'Souza RC, Cox J et al (2010) Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 9(12):6786-6794
32. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purifi cation, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2(8):1896-1906
33. Ishihama Y, Rappsilber J, Andersen JS et al (2002) Microcolumns with self-assembled particle frits for proteomics. J Chromatogr A 979(1-2):233-239
34. Geiger T, Cox J, Ostasiewicz P et al (2011) Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 7(5):383-385
35. Rigbolt KT, Blagoev B (2010) Proteome-wide quantitation by SILAC. Methods Mol Biol 658:187-204
36. Nielsen ML, Vermeulen M, Bonaldi T et al (2008) Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat Methods 5(6):459-460
37. Kelstrup CD, Hekmat O, Francavilla C et al (2011) Pinpointing phosphorylation sites: quantitative fi ltering and a novel site-specifi c x-ion fragment. J Proteome Res 10(7):2937-2948
38. Sugiyama N, Masuda T, Shinoda K et al (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modifi ed metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics 6(6):1103-1109
39. Zhou H, Low TY, Hennrich ML et al (2011) Enhancing the identifi cation of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics 10(10):M110.006452
40. Francavilla C, Rigbolt KT, Emdal KB et al (2013) Functional proteomics defi nes the molecular switch underlying FGF receptor traffi cking and cellular outputs. Mol Cell 51(6): 707-722