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Home arrow Health arrow Analysis of Protein Post-Translational Modifications by Mass Spectrometry



Acetylation and methylation PTMs are key regulatory events subject to research using mass spectrometry and related biochemical techniques. This chapter aims to capture the key findings and developments in the field in terms of identification, characterization, and monitoring of quantitative changes in different biological states.


  • 1 Shemorry A, Hwang CS, Varshavsky A. Control of protein quality and stoichiometries by N-terminal acetylation and the N-end rule pathway. Mol Cell 2013;50:540-551.
  • 2 Choudhary C, Weinert BT, Nishida Y, Verdin E, Mann M. The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 2014;15:536-550.
  • 3 Biggar KK, Li SS. Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 2015;16:5-17.
  • 4 Su X, Wellen KE, Rabinowitz JD. Metabolic control of methylation and acetylation. Curr Opin Chem Biol 2016;30:52-60.
  • 5 Venne AS, Kollipara L, Zahedi RP. The next level of complexity: crosstalk of post-translational modifications. Proteomics 2014;14:513-524.
  • 6 Szabo Z, Janaky T. Challenges and developments in protein identification using mass spectrometry. Trends Anal Chem 2015;69:76-87.
  • 7 Kouzarides T. Acetylation: a regulatory modification to rival phosphorylation? EMBO J 2000;19:1176-1179.
  • 8 Ng MK, Cheung P. A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context. Biochem Cell Biol 2015;94:33-42.
  • 9 Schilling B, Christensen D, Davis R, Sahu AK, Hu LI, Walker-Peddakotla A, Sorensen DJ, Zemaitaitis B, Gibson BW, Wolfe AJ. Protein acetylation dynamics in response to carbon overflow in Escherichia coli. Mol Microbiol 2015;98:847-863.
  • 10 Varland S, Osberg C, Arnesen T. N-terminal modifications of cellular proteins: the enzymes involved, their substrate specificities and biological effects. Proteomics 2015;15:2385-2401.
  • 11 Afjehi-Sadat L, Garcia BA. Comprehending dynamic protein methylation with mass spectrometry. Curr Opin Chem Biol 2013;17:12-19.
  • 12 Whetstine JR. Methylation: a multifaceted modification - looking at transcription and beyond. Biochim Biophys Acta 2014;1839:1351-1352.
  • 13 Tikhanovich I, Kuravi S, Artigues A, Villar MT, Dorko K, Nawabi A, Roberts B, Weinman SA. Dynamic arginine methylation of tumor necrosis factor (TNF) receptor-associated factor 6 regulates toll-like receptor signalling. J Biol Chem 2015;290:22236-22249.
  • 14 Declerck K, Vel Szic KS, Palagani A, Heyninck K, Haegeman G, Morand C, Milenkovic D, Berghe WV. Epigenetic control of cardiovascular health by nutritional polyphenols involves multiple chromatin-modifying writer-reader- eraser proteins. Curr Top Med Chem 2016;16:788-806.
  • 15 Gayatri S, Bedford MT. Readers of histone methylarginine marks. Biochim Biophys Acta 2014;1839:702-10.
  • 16 Sanchez R, Meslamani J, Zhou MM. The bromodomain: from epigenome reader to druggable target. Biochim Biophys Acta 2014;1839:676-85.
  • 17 Kaniskan HU, Konze KD, Jin J. Selective inhibitors of protein methyltransferases. J Med Chem 2015;58:1596-629.
  • 18 Van Dyke MW. Lysine deacetylase (KDAC) regulatory pathways: an alternative approach to selective modulation. ChemMedChem 2014;9:511-22.
  • 19 Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA. Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow. Mol Cell Proteomics 2015;14:2429-2440.
  • 20 Smith LM, Kelleher NL. Proteoform: a single term describing protein complexity. Nat Methods 2013;10:186-187.
  • 21 Xiong L, Adhvaryu KK, Selker EU, Wang Y. Mapping of lysine methylation and acetylation in core histones of Neurospora crassa. Biochemistry 2010;49:5236-5243.
  • 22 Quan, L., Liu, M.: CID, ETD and HCD fragmentation to study protein post-translational modifications. Mod Chem Appl 1, e102 (2013).
  • 23 Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein post-translational modifications. ACS Chem Biol 2014;10:63-71.
  • 24 Moradian A, Kalli A, Sweredoski MJ, Hess S. The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. Proteomics 2014;14:489-497.
  • 25 Young NL, DiMaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA. High throughput characterization of combinatorial histone codes. Mol Cell Proteomics 2009;8:2266-2284.
  • 26 Mikesh LM, Ueberheide B, Chi A, Coon JJ, Syka JE, Shabanowitz J, Hunt DF. The utility of ETD mass spectrometry in proteomic analysis. Biochim Biophys Acta 2006;1764:1811-1822.
  • 27 Frese CK, Altelaar AM, Hennrich ML, Nolting D, Zeller M, Griep-Raming J, Heck AJ, Mohammed S. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos.

J Proteome Res 2011;10:2377-2388.

  • 28 Wang H, Straubinger RM, Aletta JM, Cao J, Duan X, Yu H, Qu J. Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry. J Am Soc Mass Spectrom 2009;20:507-519.
  • 29 Jufvas, A., Stralfors, P., Vener, A.V.: Histone variants and their post-translational modifications in primary human fat cells. PLoS One 6, e15960 (2011).
  • 30 Zhang K, Yau PM, Chandrasekhar B, New R, Kondrat R, Imai BS, Bradbury ME. Differentiation between peptides containing acetylated or trimethylated lysines by mass spectrometry: an application for determining lysine 9 acetylation and methylation of histone H3. Proteomics 2004;4:1-10.
  • 31 Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 2007;4:709-712.
  • 32 Matthiesen R, Trelle MB, Hojrup P, Bunkenborg J, Jensen ON. VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res 2005;4:2338-2347.
  • 33 Kelstrup CD, Frese C, Heck AJ, Olsen JV, Nielsen ML. Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). Mol Cell Proteomics 2014;13:1914-1924.
  • 34 Karch KR, Zee BM, Garcia BA. High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. J Proteome Res 2014;13:6152-6159.
  • 35 Trelle MB, Jensen ON. Utility of immonium ions for assignment of epsilon-N- acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem 2008;80:3422-3430.
  • 36 Fu L, Chen T, Xue G, Zu L, Fang W. Selective cleavage enhanced by acetylating the side chain of lysine. J Am Soc Mass Spectrom 2013;48:128-134.
  • 37 Couttas TA, Raftery MJ, Bernardini G, Wilkins MR. Immonium ion scanning for the discovery of post-translational modifications and its application to histones. J Proteome Res 2008;7:2632-2641.
  • 38 Gehrig PM, Hunziker PE, Zahariev S, Pongor S. Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS. J Am Soc Mass Spectrom 2004;15:142-149.
  • 39 Ong SE, Mittler G, Mann M. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods 2004;1:119-126.
  • 40 Brame CJ, Moran MF, McBroom-Cerajewski LD. A mass spectrometry based method for distinguishing between symmetrically and asymmetrically dimethylated arginine residues. Rapid Commun Mass Spectrom 2004;18:877-881.
  • 41 Rappsilber J, Friesen WJ, Paushkin S, Dreyfuss G, Mann M. Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion mode. Anal Chem 2003;75:3107-3114.
  • 42 Snijders AP, Hung ML, Wilson SA, Dickman MJ. Analysis of arginine and lysine methylation utilizing peptide separations at neutral pH and electron transfer dissociation mass spectrometry. J Am Soc Mass Spectrom 2010;21:88-96.
  • 43 Hung CW, Schlosser A, Wei J, Lehmann WD. Collision-induced reporter fragmentations for identification of covalently modified peptides. Anal Bioanal Chem 2007;389:1003-1016.
  • 44 Hirota J, Satomi Y, Yoshikawa K, Takao T. e-N,N,N-Trimethyllysine-specific ions in matrix-assisted laser desorption/ionization-tandem mass spectrometry. Rapid Commun Mass Spectrom 2003;17:371-376.
  • 45 Hart-Smith G, Low JK, Erce MA, Wilkins MR. Enhanced methylarginine characterization by post-translational modification-specific targeted data acquisition and electron-transfer dissociation mass spectrometry. J Am Soc Mass Spectrom 2012;23:1376-1389.
  • 46 Geoghegan V, Guo A, Trudgian D, Thomas B, Acuto O. Comprehensive identification of arginine methylation in primary T cells reveals regulatory roles in cell signalling. Nat Commun 2015;7:6758-6766.
  • 47 Unwin RD, Griffiths JR, Whetton AD. A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS). Nat Protoc 2009;4:870-877.
  • 48 Griffiths JR, Unwin RD, Evans CA, Leech SH, Corfe BM, Whetton AD. The application of a hypothesis-driven strategy to the sensitive detection and location of acetylated lysine residues. J Am Soc Mass Spectrom 2007;18:1423-1428.
  • 49 Borchers C, Parker CE, Deterding LJ, Tomer KB. Preliminary comparison of precursor scans and liquid chromatography-tandem mass spectrometry on a hybrid quadrupole time-of-flight mass spectrometer. J Chromatogr A 1999;854:119-130.
  • 50 Kim JY, Kim KW, Kwon HJ, Lee DW, Yoo JS. Probing lysine acetylation with a modification-specific marker ion using high-performance liquid chromatography/electrospray-mass spectrometry with collision-induced dissociation. Anal Chem 2002;74:5443-5449.
  • 51 Evans CA, Ow SY, Smith DL, Corfe BM, Wright PC. Application of the CIRAD mass spectrometry approach for lysine acetylation site discovery. Methods Mol Biol 2013;981:13-23.
  • 52 Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D. Bottom-up proteomics (2013-2015): keeping up in the era of systems biology. Anal Chem 2015;88:95-121.
  • 53 Higgs RE, Butler JP, Han B, Knierman MD. Quantitative proteomics via high resolution MS quantification: capabilities and limitations. Int J Proteomics 2013;2013(674282).
  • 54 Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 2005;35:265-273.
  • 55 Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 2012;9:555-566.
  • 56 Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Huttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014;13:907-917.
  • 57 Colangelo CM, Chung L, Bruce C, Cheung KH. Review of software tools for design and analysis of large scale MRM proteomic datasets. Methods 2013;61:287-298.
  • 58 Sherrod SD, Myers MV, Li M, Myers JS, Carpenter KL, Maclean B, Maccoss MJ, Liebler DC, Ham AJ. Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides.

J Proteome Res 2012;11:3467-3479.

  • 59 Lin S, Wein S, Gonzales-Cope M, Otte GL, Yuan ZF, Afjehi-Sadat L, Maile T, Berger SL, Rush J, Lill JR, Arnott D, Garcia BA. Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. Mol Cell Proteomics 2014;13:2450-2466.
  • 60 Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008;4:222-236.
  • 61 Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics 2012;11:475-488.
  • 62 Tang H, Fang H, Yin E, Brasier AR, Sowers LC, Zhang K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal Chem 2014;86:5526-5534.
  • 63 Sowers JL, Mirfattah B, Xu P, Tang H, Park IY, Walker C, Wu P, Laezza F, Sowers LC, Zhang K. Quantification of histone modifications by parallel- reaction monitoring: a method validation. Anal Chem 2015;87:10006-10014.
  • 64 Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI. DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 2015;12:258-264.
  • 65 Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW. MS1 peptide ion intensity chromatograms in MS2 (SWATH) data independent acquisitions. Improving post acquisition analysis of proteomic experiments. Mol Cell Proteomics 2015;14:2405-2419.
  • 66 Geiger T, Cox J, Mann M. Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol Cell Proteomics 2010;9:2252-2261.
  • 67 Li G-Z, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009;9:1696-1719.
  • 68 Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA. Sequential window acquisition of all theoretical mass spectra (SWATH) analysis for characterization and quantification of histone posttranslational modifications. Mol Cell Proteomics 2015;14:2420-2428.
  • 69 Krautkramer KA, Reiter L, Denu JM, Dowell JA. Quantification of SAHA- dependent changes in histone modifications using data-independent acquisition mass spectrometry. JProteome Res 2015;14:3252-3262.
  • 70 Srebalus B, Hilderbrand AE, Valentine SJ, Clemmer DE. Resolving isomeric peptide mixtures: a combined HPLC/ion mobility-TOFMS analysis of a 4000- component combinatorial library. Anal Chem 2002;74:26-36.
  • 71 Gethings LA, Connolly JB. Simplifying the proteome: analytical strategies for improving peak capacity. Adv Exp Med Biol 2014;806:59-77.
  • 72 Rodriguez-Suarez E, Hughes C, Gethings L, Giles K, Wildgoose J, Stapels M, Fadgen KE, Geromanos SJ, Vissers JP, Elortza F, Langridge JI. An ion mobility assisted data independent LC-MS strategy for the analysis of complex biological samples. Curr Anal Chem 2013;9:199-211.
  • 73 Shliaha PV, Bond NJ, Gatto L, Lilley KS. Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies. J Proteome Res 2013;12:2323-2339.
  • 74 Shliaha PV, Jukes-Jones R, Christoforou A, Fox J, Hughes C, Langridge J, Cain K, Lilley KS. Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS). J Proteome Res 2014;13:3360-3369.
  • 75 Helm D, Vissers JP, Hughes CJ, Hahne H, Ruprecht B, Pachl F, Grzyb A, Richardson K, Wildgoose J, Maier SK, Marx H, Wilhelm M, Becher I, Lemeer S, Bantscheff M, Langridge JI, Kuster B. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014;13:3709-3715.
  • 76 Donohoe GC, Maleki H, Arndt JR, Khakinejad M, Yi J, McBride C, Nurkiewicz TR, Valentine SJ. A new ion mobility-linear ion trap instrument for complex mixture analysis. Anal Chem 2014;86:8121-8128.
  • 77 Lermyte F, Williams JP, Brown JM, Martin EM, Sobott F. Extensive charge reduction and dissociation of intact protein complexes following electron transfer on a quadrupole-ion mobility-time-of-flight MS. J Am Soc Mass Spectrom 2015;26:1068-1076.
  • 78 Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Ion mobility separation of variant histone tails extending to the "middle-down" range. Anal Chem 2012;84:4271-4276.
  • 79 Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. Quantitative dynamics of the link between cellular metabolism and histone acetylation. J Biol Chem 2013;288:12142-12151.
  • 80 Zheng Y, Sweet SM, Popovic R, Martinez-Garcia E, Tipton JD, Thomas PM, Licht JD, Kelleher NL. Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3. Proc Natl Acad Sci U S A 2012;109:13549-13554.
  • 81 Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 2010;3:ra3.
  • 82 Nakayasu ES, Wu S, Sydor MA, Shukla AK, Weitz KK, Moore RJ, Hixson KK, Kim JS, Petyuk VA, Monroe ME, Pasa-Tolic L, Qian WJ, Smith RD, Adkins JN, Ansong C. A method to determine lysine acetylation stoichiometries. Int J Proteomics 2014;2014:730725.
  • 83 Hersman E, Nelson DM, Griffith WP, Jelinek C, Cotter RJ. Analysis of histone modifications from tryptic peptides of deuteroacetylated isoforms. Int J Mass Spectrom 2012;312:5-16.
  • 84 Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM. Stoichiometry of site-specific lysine acetylation in an entire proteome.

J Biol Chem 2014;289:21326-21338.

  • 85 Pesavento JJ, Mizzen CA, Kelleher NL. Quantitative analysis of modified proteins and their positional isomers by tandem mass spectrometry: human histone H4. Anal Chem 2006;78:4271-4280.
  • 86 Tipton, J.D., Tran, J.C., Catherman, A.D., Ahlf, D.R., Durbin, K.R., Kelleher, N.L.: Analysis of intact protein isoforms by mass spectrometry. JBiol Chem 2011;286, 25451-25458.
  • 87 Tran JC, Zamdborg L, Ahlf DR, Lee JE, Catherman AD, Durbin KR, Tipton JD, Vellaichamy A, Kellie JF, Li M, Wu C, Sweet SM, Early BP, Siuti N, LeDuc RD, Compton PD, Thomas PM, Kelleher NL. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 2011;480:254-25.
  • 88 Durbin KR, Tran JC, Zamdborg L, Sweet SM, Catherman AD, Lee JE, Li M, Kellie JF, Kelleher NL. Intact mass detection, interpretation, and visualization to automate top-down proteomics on a large scale. Proteomics 2010;10:3589-3597.
  • 89 Xiu L, Valeja SG, Alpert AJ, Jin S, Ge Y. Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal Chem 2014;86:7899-7906.
  • 90 Cannon J, Lohnes K, Wynne C, Wang Y, Edwards N, Fenselau C. High- throughput middle-down analysis using an orbitrap. JProteome Res 2010;9:3886-3890.
  • 91 Wiesner J, Premsler T, Sickmann A. Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 2008;8:4466-4483.
  • 92 Sweredoski MJ, Moradian A, Raedle M, Franco C, Hess S. High resolution parallel reaction monitoring with electron transfer dissociation for middle- down proteomics. Anal Chem 2015;87:8360-8366.
  • 93 Bryson BD, Del Rosario AM, Gootenberg JS, Yaffe MB, White FM. Engineered bromodomains to explore the acetylproteome. Proteomics 2015;15:1470-1475.
  • 94 Andersen JL, Thompson JW, Lindblom KR, Johnson ES, Yang CS, Lilley LR, Freel CD, Moseley MA, Kornbluth S. A biotin switch-based proteomics approach identifies 14-3-3Z as a target of Sirt1 in the metabolic regulation of caspase-2. Mol Cell 2011;43:834-842.
  • 95 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC,

Olsen JV, Mann M. Lysine acetylation targets protein complexes and coregulates major cellular functions. Science 2009;325:834-840.

  • 96 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA. Integrated proteomic analysis of posttranslational modifications by serial enrichment. Nat Methods 2013;10:634-637.
  • 97 Uhlmann T, Geoghegan VL, Thomas B, Ridlova G, Trudgian DC, Acuto O.

A method for large-scale identification of protein arginine methylation. Mol Cell Proteomics 2012;11:1489-1499.

  • 98 Plank M, Fischer R, Geoghegan V, Charles PD, Konietzny R, Acuto O, Pears C, Schofield CJ, Kessler BM. Expanding the yeast protein arginine methylome. Proteomics 2015;15:3232-3243.
  • 99 Boisvert FM, Cote J, Boulanger MC, Richard S. A proteomic analysis of arginine-methylated protein complexes. Mol Cell Proteomics 2003;2:1319-1330.
  • 100 Guo A, Gu H, Zhou J, Mulhern D, Wang Y, Lee KA, Yang V, Aguiar M, Kornhauser J, Jia X, Ren J, Beausoleil SA, Silva JC, Vemulapalli V, Bedford MT, Comb MJ. Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol Cell Proteomics 2014;13:372-387.
  • 101 Cao XJ, Arnaudo AM, Garcia BA. Large-scale global identification of protein lysine methylation in vivo. Epigenetics 2013;8:477-485.
  • 102 Carlson SM, Gozani O. Emerging technologies to map the protein methylome. J Mol Biol 2014;426:3350-3362.
  • 103 Leech SH, Evans CA, Shaw L, Wong CH, Connolly J, Griffiths JR, Whetton AD, Corfe BM. Proteomic analyses of intermediate filaments reveals cytokeratin8 is highly acetylated - implications for colorectal epithelial homeostasis. Proteomics 2008;8:279-288.
  • 104 Champleboux M, Govin J. Bromodomains shake the hegemony of pan-acetyl antibodies. Proteomics 2015;15:1457-1458.
  • 105 Moore KE, Carlson SM, Camp ND, Cheung P, James RG, Chua KF, Wolf- Yadlin A, Gozani O. A general molecular affinity strategy for global detection and proteomic analysis of lysine methylation. Mol Cell 2013;50:444-456.
  • 106 Carlson SM, Moore KE, Green EM, Martin GM, Gozani O. Proteome-wide enrichment of proteins modified by lysine methylation. Nat Protoc 2014;9:37-50.
  • 107 Liu H, Galka M, Mori E, Liu X, Lin YF, Wei R, Pittock P, Voss C, Dhami G, Li X, Miyaji M, Lajoie G, Chen B, Li SS. A method for systematic mapping of protein lysine methylation identifies functions for HP1p in DNA damage response. Mol Cell 2013;50:723-735.
  • 108 Jaffrey SR, Snyder SH. The biotin switch method for the detection of S-nitrosylated proteins. Sci STKE 2001;pl1.
  • 109 Thompson JW, Robeson A, Andersen JL. Identification of deacetylase substrates with the biotin switch approach. Methods Mol Biol 2013;1077:133-148.
  • 110 Taouatas N, Mohammed S, Heck AJ. Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics. Methods Mol Biol 2011;753:157-167.
  • 111 Chen SH, Chen CR, Chen SH, Li DT, Hsu JL. Improved Na-acetylated peptide enrichment following dimethyl labeling and SCX. J Proteome Res 2013;12:3277-3287.
  • 112 Noble, W.S., MacCoss, M.J.: Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol 2012;8:e1002296.
  • 113 Kim MS, Zhong J, Pandey A. Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics; 2015. DOI: 10.1002/ pmic.201500355.
  • 114 Fu Y, Qian X. Transferred subgroup false discovery rate for rare posttranslational modifications detected by mass spectrometry. Mol Cell Proteomics 2014;13:1359-1368.
  • 115 Creasy DM, Cottrell JS. Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics 2002;2:1426-1434.
  • 116 Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004;20:1466-1467.
  • 117 Kertesz-Farkas A, Keich U, Noble WS. Improved false discovery rate estimation procedure for shotgun proteomics. J Proteome Res 2015;14:3148-3161.
  • 118 Yuan ZF, Lin S, Molden RC, Garcia BA. Evaluation of proteomic search engines for the analysis of histone modifications. J Proteome Res 2014;13:4470-4478.
  • 119 Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Kall L, Aebersold R, Smith RD, Noble WS, MacCoss MJ. Peptide-centric proteome analysis: an alternative strategy for the analysis of tandem mass spectrometry data.

Mol Cell Proteomics 2015;14:2301-2307.

  • 120 Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 2015;43:D512-D520.
  • 121 Li J, Jia J, Li H, Yu J, Sun H, He Y, Lv D, Yang X, Glocker MO, Ma L, Yang J. SysPTM 2.0: an updated systematic resource for post-translational modification. Database 2014:bau025.
  • 122 Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J. Bork, P: PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res 2014;43(D1):D494-D502.
  • 123 Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res 2015;43(D1):D521-D530.
  • 124 Shi SP, Xu HD, Wen PP, Qiu JD. 2015. Progress and challenges in predicting protein methylation sites. Mol. BioSystems 2015;11:2610-2619.
  • 125 Hou T, Zheng G, Zhang P, Jia J, Li J, Xie L, Wei C, Li Y. LAceP: lysine acetylation site prediction using logistic regression classifiers. PLoS One 2014;9:e89575.
  • 126 Cesaro L, Pinna LA, Salvi M. A comparative analysis and review of lysyl residues affected by post-translational modifications. Curr Genomics 2015;16:128-138.
  • 127 Li T, Du Y, Wang L, Huang L, Li W, Lu M, Zhang X, Zhu WG. Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites. Mol Cell Proteomics 2012;11:M111-011080.
  • 128 Chuh KN, Pratt MR. Chemical methods for the proteome-wide identification of post-translationally modified proteins. Curr Opin Chem Biol 2015;24:27-37.
  • 129 Blum G, Bothwell IR, Islam K, Luo M. Profiling protein methylation with cofactor analog containing terminal alkyne functionality. Curr Protocols Chem Biol 2013;5:67-88.
  • 130 Yap MC, Kostiuk MA, Martin DD, Perinpanayagam MA, Hak PG, Siddam A, Majjigapu JR, Rajaiah G, Keller BO, Prescher JA, Wu P. Rapid and selective detection of fatty acylated proteins using w-alkynyl-fatty acids and click chemistry. J Lipid Res 2010;51:1566-1580.
  • 131 Hennrich ML, Gavin AC. Quantitative mass spectrometry of post-translational modifications: keys to confidence. Sci Signal 2015;8:re5.
  • 132 Schmidt A, Forne I, Imhof A. Bioinformatic analysis of proteomics data. BMC Syst Biol 2014;8:S3.
  • 133 Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional crosstalk of protein post-translational modifications. Mol Syst Biol 2013;9:714.
  • 134 Lu, Z., Cheng, Z., Zhao, Y., Volchenboum, S.L.: Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PLoS One 2011;6:e28228.
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