1932

Abstract

Histones play important roles in chromatin, in the forms of various posttranslational modifications (PTMs) and sequence variants, which are called histone proteoforms. Investigating modifications and variants is an ongoing challenge. Previous methods are based on antibodies, and because they usually detect only one modification at a time, they are not suitable for studying the various combinations of modifications on histones. Fortunately, mass spectrometry (MS) has emerged as a high-throughput technology for histone analysis and does not require prior knowledge about any modifications. From the data generated by mass spectrometers, both identification and quantification of modifications, as well as variants, can be obtained easily. On the basis of this information, the functions of histones in various cellular contexts can be revealed. Therefore, MS continues to play an important role in the study of histone proteoforms. In this review, we discuss the analysis strategies of MS, their applications on histones, and some key remaining challenges.

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2014-06-12
2024-04-17
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Literature Cited

  1. Smith LM, Kelleher NL. 1.  2013. Proteoform: a single term describing protein complexity. Nat. Methods 10:186–87 [Google Scholar]
  2. Arnaudo AM, Garcia BA. 2.  2013. Proteomic characterization of novel histone post-translational modifications. Epigenet. Chromatin 6:24–30 [Google Scholar]
  3. Arnaudo AM, Molden RC, Garcia BA. 3.  2011. Revealing histone variant induced changes via quantitative proteomics. Crit. Rev. Biochem. Mol. Biol. 46:284–94 [Google Scholar]
  4. Cheung P.4.  2004. Generation and characterization of antibodies directed against di-modified histones, and comments on antibody and epitope recognition. Methods Enzymol. 376:221–34 [Google Scholar]
  5. Britton LM, Gonzales-Cope M, Zee BM, Garcia BA. 5.  2011. Breaking the histone code with quantitative mass spectrometry. Expert Rev. Proteomics 8:631–43 [Google Scholar]
  6. Andersson C-O.6.  1958. Mass spectrometric studies on amino acid and peptide derivatives. Acta Chem. Scand. 12:1353 [Google Scholar]
  7. Dass C.7.  2007. Fundamentals of Contemporary Mass Spectrometry Hoboken, NJ: Wiley
  8. Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. 8.  1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71 [Google Scholar]
  9. Tanaka K, Waki H, Ido Y, Akita S, Yoshida Y. 9.  et al. 1988. Protein and polymer analyses up to m/z 100 000 by laser ionization time-of flight mass spectrometry. Rapid Commun. Mass Spectrom. 2:151–53 [Google Scholar]
  10. Wells JM, McLuckey SA. 10.  2005. Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol. 402:148–85 [Google Scholar]
  11. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. 11.  2004. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101:9528–33 [Google Scholar]
  12. Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA. 12.  1999. De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. 6:327–42 [Google Scholar]
  13. Ma B, Zhang K, Hendrie C, Liang C, Li M. 13.  et al. 2003. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 17:2337–42 [Google Scholar]
  14. Taylor JA, Johnson RS. 14.  1997. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 11:1067–75 [Google Scholar]
  15. Eng JK, McCormack AL, John R, Yates I. 15.  1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976–89 [Google Scholar]
  16. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. 16.  1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–67 [Google Scholar]
  17. Craig R, Beavis RC. 17.  2004. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466–67 [Google Scholar]
  18. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M. 18.  et al. 2004. Open mass spectrometry search algorithm. J. Proteome Res. 3:958–64 [Google Scholar]
  19. Bern M, Cai Y, Goldberg D. 19.  2007. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal. Chem. 79:1393–400 [Google Scholar]
  20. Fu Y, Xiu LY, Jia W, Ye D, Sun RX. 20.  et al. 2011. DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data. Mol. Cell Proteomics 10:M110.000455 [Google Scholar]
  21. Ye D, Fu Y, Sun RX, Wang HP, Yuan ZF. 21.  et al. 2010. Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 26:i399–i406 [Google Scholar]
  22. Smith CM, Haimberger ZW, Johnson CO, Wolf AJ, Gafken PR. 22.  et al. 2002. Heritable chromatin structure: mapping “memory” in histones H3 and H4. Proc. Natl. Acad. Sci. USA 99:Suppl. 416454–61 [Google Scholar]
  23. Smith CM, Gafken PR, Zhang Z, Gottschling DE, Smith JB, Smith DL. 23.  2003. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal. Biochem. 316:23–33 [Google Scholar]
  24. Bonaldi T, Imhof A, Regula JT. 24.  2004. A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications. Proteomics 4:1382–96 [Google Scholar]
  25. Peters AH, Kubicek S, Mechtler K, O'Sullivan RJ, Derijck AA. 25.  et al. 2003. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12:1577–89 [Google Scholar]
  26. Syka JE, Marto JA, Bai DL, Horning S, Senko MW. 26.  et al. 2004. Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3:621–26 [Google Scholar]
  27. Garcia BA, Mollah S, Ueberheide BM, Busby SA, Muratore TL. 27.  et al. 2007. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2:933–38 [Google Scholar]
  28. Hoopmann MR, Finney GL, MacCoss MJ. 28.  2007. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal. Chem. 79:5620–32 [Google Scholar]
  29. Park K, Yoon JY, Lee S, Paek E, Park H. 29.  et al. 2008. Isotopic peak intensity ratio based algorithm for determination of isotopic clusters and monoisotopic masses of polypeptides from high-resolution mass spectrometric data. Anal. Chem. 80:7294–303 [Google Scholar]
  30. Cox J, Mann M. 30.  2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26:1367–72 [Google Scholar]
  31. Yuan ZF, Liu C, Wang HP, Sun RX, Fu Y. 31.  et al. 2012. pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics 12:226–35 [Google Scholar]
  32. Niu M, Mao X, Ying W, Qin W, Zhang Y, Qian X. 32.  2012. Determination of monoisotopic masses of chimera spectra from high-resolution mass spectrometric data by use of isotopic peak intensity ratio modeling. Rapid Commun. Mass Spectrom. 26:1875–86 [Google Scholar]
  33. Senko MW, Beu SC, McLafferty FW. 33.  1995. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6:229–33 [Google Scholar]
  34. Senko MW, Beu SC, McLafferty FW. 34.  1995. Automated assignment of charge states from resolved isotopic peaks for multiply charged ions. J. Am. Soc. Mass Spectrom. 6:52–56 [Google Scholar]
  35. Horn DM, Zubarev RA, McLafferty FW. 35.  2000. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J. Am. Soc. Mass Spectrom. 11:320–32 [Google Scholar]
  36. Anzilotti C, Pratesi F, Tommasi C, Migliorini P. 36.  2010. Peptidylarginine deiminase 4 and citrullination in health and disease. Autoimmun. Rev. 9:158–60 [Google Scholar]
  37. Tan M, Luo H, Lee S, Jin F, Yang JS. 37.  et al. 2011. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–28 [Google Scholar]
  38. Lundgren DH, Hwang SI, Wu L, Han DK. 38.  2010. Role of spectral counting in quantitative proteomics. Expert Rev. Proteomics 7:39–53 [Google Scholar]
  39. Heinecke NL, Pratt BS, Vaisar T, Becker L. 39.  2010. PepC: proteomics software for identifying differentially expressed proteins based on spectral counting. Bioinformatics 26:1574–75 [Google Scholar]
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