SILAC-based quantitative strategies for accurate histone posttranslational modification profiling across multiple biological samples

Methods in Molecular Biology

Volumn 1528, Issue , 2017, Pages 97-119

  Cuomo, Alessandro ^a   Soldi, Monica ^a   Bonaldi, Tiziana ^a  

^a EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

Author keywords

Epigenetics; High resolution mass spectrometry; Histone posttranslational modifications; SILAC; SILAC spike in; Ultrahigh pressure liquid chromatography

Indexed keywords

HISTONE;

EPIGENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOTOPE LABELING; METABOLISM; PROCEDURES; PROTEIN PROCESSING;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; EPIGENOMICS; HISTONES; ISOTOPE LABELING; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 84995902667     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6630-1_7     Document Type: Chapter

References (45)

1. Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
2. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
3. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080
4. Tan M, Luo H, Lee S et al (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028
5. Garcia BA, Shabanowitz J, Hunt DF (2007) Characterization of histones and their posttranslational modifications by mass spectrometry. Curr Opin Chem Biol 11:66–73
6. Sidoli S, Cheng L, Jensen ON (2012) Proteomics in chromatin biology and epigenetics: elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics 75:3419–3433
7. Britton LM, Gonzales-Cope M, Zee BM, Garcia BA (2011) Breaking the histone code with quantitative mass spectrometry. Expert Rev Proteomics 8:631–643
8. Pesavento JJ, Bullock CR, LeDuc RD, Mizzen CA, Kelleher NL (2008) Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry. J Biol Chem 283:14927–14937
9. Pesavento JJ, Mizzen CA, Kelleher NL (2006) Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4. Anal Chem 78:4271–4280
10. Plazas-Mayorca MD, Zee BM, Young NL et al (2009) One-pot shotgun quantitative mass spectrometry characterization of histones. J Proteome Res 8:5367–5374
11. Shukla AK, Futrell JH (2000) Tandem mass spectrometry: dissociation of ions by collisional activation. J Mass Spectrom 35:1069–1090
12. Jung HR, Pasini D, Helin K, Jensen ON (2010) Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol Cell Proteomics 9:838–850
13. Olsen JV, Macek B, Lange O et al (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 4:709–712
14. Soldi M, Cuomo A, Bremang M, Bonaldi T (2013) Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. Int J Mol Sci 14:5402–5431
15. Cuomo A, Moretti S, Minucci S, Bonaldi T (2011) SILAC-based proteomic analysis to dissect the “histone modification signature” of human breast cancer cells. Amino Acids 41:387–399
16. Sidoli S, Schwammle V, Ruminowicz C et al (2014) Middle-down hybrid chromatography/ tandem mass spectrometry workflow for characterization of combinatorial posttranslational modifications in histones. Proteomics 14:2200–2211
17. Jung HR, Sidoli S, Haldbo S et al (2013) Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Anal Chem 85:8232–8239
18. Young NL, DiMaggio PA, Plazas-Mayorca MD et al (2009) High throughput characterization of combinatorial histone codes. Mol Cell Proteomics 8:2266–2284
19. Zee BM, Young NL, Garcia BA (2011) Quantitative proteomic approaches to studying histone modifications. Curr Chem Genomics 5:106–114
20. Eberl HC, Mann M, Vermeulen M (2011) Quantitative proteomics for epigenetics. Chembiochem 12:224–234
21. 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 1:376–386
22. Ong SE, Mann M (2006) A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 1:2650–2660
23. Ong SE, Mann M (2007) Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol 359:37–52
24. Geiger T, Wisniewski JR, Cox J et al (2011) Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc 6:147–157
25. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2:1896–1906
26. Olsen JV, Ong SE, Mann M (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics 3:608–614
27. Thakur SS, Geiger T, Chatterjee B et al (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol Cell Proteomics 10:M110.003699
28. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome- wide protein quantification. Nat Biotechnol 26: 1367–1372
29. Kirchner M, Selbach M (2012) In vivo quantitative proteome profiling: planning and evaluation of SILAC experiments. Methods Mol Biol 893:175–199
30. Pozniak Y, Geiger T (2014) Design and application of super-SILAC for proteome quantifi- cation. Methods Mol Biol 1188:281–291
31. Shenoy A, Geiger T (2015) Super-SILAC: current trends and future perspectives. Expert Rev Proteomics 12:1–7
32. Bremang M, Cuomo A, Agresta AM et al (2013) Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. Mol Biosyst 9:2231–2247
33. Boersema PJ, Mohammed S, Heck AJ (2008) Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem 391:151–159
34. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1:2856–2860
35. Soldi M, Bonaldi T (2014) The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin. J Vis Exp. doi:10.3791/51220
36. Soldi M, Cuomo A, Bonaldi T (2014) Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument. Proteomics 14:2212–2225
37. Nagaraj N, Kulak NA, Cox J et al (2012) System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics 11:M111.013722
38. Egertson JD, Kuehn A, Merrihew GE et al (2013) Multiplexed MS/MS for improved data-independent acquisition. Nat Methods 10:744–746
39. Zubarev RA, Horn DM, Fridriksson EK et al (2000) Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem 72:563–573
40. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 101:9528–9533
41. Michalski A, Neuhauser N, Cox J, Mann M (2012) A systematic investigation into the nature of tryptic HCD spectra. J Proteome Res 11:5479–5491
42. Xie Z, Dai J, Dai L et al (2012) Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics 11:100–107
43. Cox J, Neuhauser N, Michalski A et al (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10:1794–1805
44. Tyanova S, Mann M, Cox J (2014) MaxQuant for in-depth analysis of large SILAC datasets. Methods Mol Biol 1188:351–364
45. Schilling B, Rardin MJ, MacLean BX et al (2012) Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics 11:202–214