{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T23:19:03Z","timestamp":1783207143927,"version":"3.54.6"},"publisher-location":"Cham","reference-count":72,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783032216373","type":"print"},{"value":"9783032216380","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-3-032-21638-0_4","type":"book-chapter","created":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T22:53:20Z","timestamp":1783205600000},"page":"75-102","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Proteomic Analysis of Histone Sequence Variants and Post-translationally Modified Forms"],"prefix":"10.1007","author":[{"given":"Palina","family":"Ryzhaya","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavl\u00edna","family":"P\u00edrek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radom\u00edr","family":"Pech","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karol\u00edna","family":"Kry\u0161tofov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zbyn\u011bk","family":"Zdr\u00e1hal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Lochmanov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,2]]},"reference":[{"key":"4_CR1","doi-asserted-by":"publisher","unstructured":"Allfrey V, Faulkner R, Mirsky A (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 51. https:\/\/doi.org\/10.1073\/pnas.51.5.786","DOI":"10.1073\/pnas.51.5.786"},{"key":"4_CR2","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1126\/science.1063127","volume":"293","author":"T Jenuwein","year":"2001","unstructured":"Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074\u20131080. https:\/\/doi.org\/10.1126\/science.1063127","journal-title":"Science"},{"key":"4_CR3","doi-asserted-by":"publisher","unstructured":"Sun L, Zhang H, Gao P (2022) Metabolic reprogramming and epigenetic modifications on the path to cancer. Protein Cell 13. https:\/\/doi.org\/10.1007\/s13238-021-00846-7","DOI":"10.1007\/s13238-021-00846-7"},{"key":"4_CR4","doi-asserted-by":"publisher","unstructured":"Schueller E, Paiva I, Blanc F, Wang X, Cassel J, Boutillier A, Bousiges O (2020) Dysregulation of histone acetylation pathways in hippocampus and frontal cortex of Alzheimer\u2019s disease patients. Eur Neuropsychopharmacol 33. https:\/\/doi.org\/10.1016\/j.euroneuro.2020.01.015","DOI":"10.1016\/j.euroneuro.2020.01.015"},{"key":"4_CR5","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1186\/s40001-024-02108-8","volume":"29","author":"M-S Hosseini","year":"2024","unstructured":"Hosseini M-S, Sanaat Z, Akbarzadeh MA, Vaez-Gharamaleki Y, Akbarzadeh M (2024) Histone deacetylase inhibitors for leukemia treatment: current status and future directions. Eur J Med Res 29:514. https:\/\/doi.org\/10.1186\/s40001-024-02108-8","journal-title":"Eur J Med Res"},{"key":"4_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejps.2025.107057","volume":"208","author":"N El Omari","year":"2025","unstructured":"El Omari N, Bakrim S, Elhrech H, Aanniz T, Balahbib A, Lee L-H, Al Abdulmonem W, Bouyahya A (2025) Clinical efficacy and mechanistic insights of FDA-approved HDAC inhibitors in the treatment of lymphoma. Eur J Pharm Sci 208:107057. https:\/\/doi.org\/10.1016\/j.ejps.2025.107057","journal-title":"Eur J Pharm Sci"},{"key":"4_CR7","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1071\/RD14167","volume":"27","author":"AM O\u2019Doherty","year":"2015","unstructured":"O\u2019Doherty AM, McGettigan PA (2015) Epigenetic processes in the male germline. Reprod Fertil Dev 27:725\u2013738. https:\/\/doi.org\/10.1071\/RD14167","journal-title":"Reprod Fertil Dev"},{"key":"4_CR8","doi-asserted-by":"publisher","first-page":"1295","DOI":"10.1093\/hmg\/ddu540","volume":"24","author":"S Laurentino","year":"2015","unstructured":"Laurentino S, Beygo J, Nordhoff V, Kliesch S, Wistuba J, Borgmann J, Buiting K, Horsthemke B, Gromoll J (2015) Epigenetic germline mosaicism in infertile men. Hum Mol Genet 24:1295\u20131304. https:\/\/doi.org\/10.1093\/hmg\/ddu540","journal-title":"Hum Mol Genet"},{"key":"4_CR9","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1186\/s13148-015-0155-4","volume":"7","author":"L Stuppia","year":"2015","unstructured":"Stuppia L, Franzago M, Ballerini P, Gatta V, Antonucci I (2015) Epigenetics and male reproduction: the consequences of paternal lifestyle on fertility, embryo development, and children lifetime health. Clin Epigenetics 7:120. https:\/\/doi.org\/10.1186\/s13148-015-0155-4","journal-title":"Clin Epigenetics"},{"key":"4_CR10","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1002\/jcb.25170","volume":"116","author":"J Krej\u010d\u00ed","year":"2015","unstructured":"Krej\u010d\u00ed J, Stixov\u00e1 L, Pag\u00e1\u010dov\u00e1 E, Legartov\u00e1 S, Kozubek S, Lochmanov\u00e1 G, Zdr\u00e1hal Z, Sehnalov\u00e1 P, Dabravolski S, Hej\u00e1tko J, B\u00e1rtov\u00e1 E (2015) Post-translational modifications of histones in human sperm. J Cell Biochem 116:2195\u20132209. https:\/\/doi.org\/10.1002\/jcb.25170","journal-title":"J Cell Biochem"},{"key":"4_CR11","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.3390\/ijms21051621","volume":"21","author":"A Agarwal","year":"2020","unstructured":"Agarwal A, Panner Selvam MK, Baskaran S (2020) Proteomic analyses of human sperm cells: understanding the role of proteins and molecular pathways affecting male reproductive health. Int J Mol Sci 21:1621. https:\/\/doi.org\/10.3390\/ijms21051621","journal-title":"Int J Mol Sci"},{"key":"4_CR12","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1007\/s10815-018-1354-7","volume":"36","author":"SB Schon","year":"2019","unstructured":"Schon SB, Luense LJ, Wang X, Bartolomei MS, Coutifaris C, Garcia BA, Berger SL (2019) Histone modification signatures in human sperm distinguish clinical abnormalities. J Assist Reprod Genet 36:267\u2013275. https:\/\/doi.org\/10.1007\/s10815-018-1354-7","journal-title":"J Assist Reprod Genet"},{"key":"4_CR13","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1016\/j.celrep.2016.12.065","volume":"18","author":"J Ueda","year":"2017","unstructured":"Ueda J, Harada A, Urahama T, Machida S, Maehara K, Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A, Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M, Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y, Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K (2017) Testis-specific histone variant H3t gene is essential for entry into spermatogenesis. Cell Rep 18:593\u2013600. https:\/\/doi.org\/10.1016\/j.celrep.2016.12.065","journal-title":"Cell Rep"},{"key":"4_CR14","doi-asserted-by":"publisher","first-page":"2808","DOI":"10.1073\/pnas.0406060102","volume":"102","author":"I Martianov","year":"2005","unstructured":"Martianov I, Brancorsini S, Catena R, Gansmuller A, Kotaja N, Parvinen M, Sassone-Corsi P, Davidson I (2005) Polar nuclear localization of H1T2, a histone H1 variant, required for spermatid elongation and DNA condensation during spermiogenesis. Proc Natl Acad Sci 102:2808\u20132813. https:\/\/doi.org\/10.1073\/pnas.0406060102","journal-title":"Proc Natl Acad Sci"},{"key":"4_CR15","doi-asserted-by":"publisher","first-page":"1680","DOI":"10.1101\/gad.220095.113","volume":"27","author":"E Montellier","year":"2013","unstructured":"Montellier E, Boussouar F, Rousseaux S, Zhang K, Buchou T, Fenaille F, Shiota H, Debernardi A, H\u00e9ry P, Curtet S, Jamshidikia M, Barral S, Holota H, Bergon A, Lopez F, Guardiola P, Pernet K, Imbert J, Petosa C, Tan M, Zhao Y, G\u00e9rard M, Khochbin S (2013) Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev 27:1680\u20131692. https:\/\/doi.org\/10.1101\/gad.220095.113","journal-title":"Genes Dev"},{"key":"4_CR16","doi-asserted-by":"publisher","first-page":"414","DOI":"10.2164\/jandrol.05171","volume":"27","author":"X Zhang","year":"2006","unstructured":"Zhang X, San Gabriel M, Zini A (2006) Sperm nuclear histone to protamine ratio in fertile and infertile men: evidence of heterogeneous subpopulations of spermatozoa in the ejaculate. J Androl 27:414\u2013420. https:\/\/doi.org\/10.2164\/jandrol.05171","journal-title":"J Androl"},{"key":"4_CR17","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1007\/s10725-022-00913-x","volume":"99","author":"J-E Guo","year":"2023","unstructured":"Guo J-E, Wang H, Yang Y, Li J, Zhu Z (2023) Histone deacetylase gene SlHDA3 is involved in drought and salt response in tomato. Plant Growth Regul 99:359\u2013372. https:\/\/doi.org\/10.1007\/s10725-022-00913-x","journal-title":"Plant Growth Regul"},{"key":"4_CR18","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1007\/s11427-024-2784-3","volume":"68","author":"Y Xue","year":"2025","unstructured":"Xue Y, Cao X, Chen X, Deng X, Deng XW, Ding Y, Dong A, Duan C-G, Fang X, Gong L, Gong Z, Gu X, He C, He H, He S, He X-J, He Y, He Y, Jia G, Jiang D, Jiang J, Lai J, Lang Z, Li C, Li Q, Li X, Liu B, Liu B, Luo X, Qi Y, Qian W, Ren G, Song Q, Song X, Tian Z, Wang J-W, Wang Y, Wu L, Wu Z, Xia R, Xiao J, Xu L, Xu Z-Y, Yan W, Yang H, Zhai J, Zhang Y, Zhao Y, Zhong X, Zhou D-X, Zhou M, Zhou Y, Zhu B, Zhu J-K, Liu Q (2025) Epigenetics in the modern era of crop improvements. Sci China Life Sci 68:1570\u20131609. https:\/\/doi.org\/10.1007\/s11427-024-2784-3","journal-title":"Sci China Life Sci"},{"key":"4_CR19","doi-asserted-by":"publisher","first-page":"4177","DOI":"10.3390\/plants12244177","volume":"12","author":"P P\u00edrek","year":"2023","unstructured":"P\u00edrek P, Kry\u0161tofov\u00e1 K, Kov\u00e1\u010dov\u00e1 I, Kromerov\u00e1 A, Zachov\u00e1 D, Helia O, Panzarov\u00e1 K, Fajkus J, Zdr\u00e1hal Z, Lochmanov\u00e1 G, Fojtov\u00e1 M (2023) Unraveling epigenetic changes in a. thaliana Calli: impact of HDAC inhibitors. Plants (Basel) 12:4177. https:\/\/doi.org\/10.3390\/plants12244177","journal-title":"Plants (Basel)"},{"key":"4_CR20","doi-asserted-by":"publisher","unstructured":"Karch KR, DeNizio JE, Black BE, Garcia BA (2013) Identification and interrogation of combinatorial histone modifications. Front Genet 4. https:\/\/doi.org\/10.3389\/fgene.2013.00264","DOI":"10.3389\/fgene.2013.00264"},{"key":"4_CR21","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2021.100114","volume":"20","author":"H Kucha\u0159\u00edkov\u00e1","year":"2021","unstructured":"Kucha\u0159\u00edkov\u00e1 H, Dobrovoln\u00e1 P, Lochmanov\u00e1 G, Zdr\u00e1hal Z (2021) Trimethylacetic anhydride-based derivatization facilitates quantification of histone marks at the MS1 level. Mol Cell Proteomics 20:100114. https:\/\/doi.org\/10.1016\/j.mcpro.2021.100114","journal-title":"Mol Cell Proteomics"},{"key":"4_CR22","doi-asserted-by":"publisher","unstructured":"Ryzhaya P, P\u00edrek P, Zdr\u00e1hal Z, Lochmanov\u00e1 G (2025) Arg-C ultra simplifies histone preparation for LC-MS\/MS. Anal Chem. https:\/\/doi.org\/10.1021\/acs.analchem.5c02238","DOI":"10.1021\/acs.analchem.5c02238"},{"key":"4_CR23","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1038\/nprot.2007.106","volume":"2","author":"BA Garcia","year":"2007","unstructured":"Garcia BA, Mollah S, Ueberheide BM, Busby SA, Muratore TL, Shabanowitz J, Hunt DF (2007) Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat Protoc 2:933\u2013938. https:\/\/doi.org\/10.1038\/nprot.2007.106","journal-title":"Nat Protoc"},{"key":"4_CR24","doi-asserted-by":"publisher","first-page":"2937","DOI":"10.1039\/c2mb25136a","volume":"8","author":"L \u010cin\u010d\u00e1rov\u00e1","year":"2012","unstructured":"\u010cin\u010d\u00e1rov\u00e1 L, Lochmanov\u00e1 G, Nov\u00e1kov\u00e1 K, \u0160ultesov\u00e1 P, Kone\u010dn\u00e1 H, Fajkusov\u00e1 L, Fajkus J, Zdr\u00e1hal Z (2012) A combined approach for the study of histone deacetylase inhibitors. Mol BioSyst 8:2937\u20132945. https:\/\/doi.org\/10.1039\/c2mb25136a","journal-title":"Mol BioSyst"},{"key":"4_CR25","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1038\/nprot.2007.202","volume":"2","author":"D Shechter","year":"2007","unstructured":"Shechter D, Dormann HL, Allis CD, Hake SB (2007) Extraction, purification and analysis of histones. Nat Protoc 2:1445\u20131457. https:\/\/doi.org\/10.1038\/nprot.2007.202","journal-title":"Nat Protoc"},{"key":"4_CR26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp273","volume":"37","author":"P Rodriguez-Collazo","year":"2009","unstructured":"Rodriguez-Collazo P, Leuba SH, Zlatanova J (2009) Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications. Nucleic Acids Res 37:e81. https:\/\/doi.org\/10.1093\/nar\/gkp273","journal-title":"Nucleic Acids Res"},{"key":"4_CR27","doi-asserted-by":"publisher","first-page":"2765","DOI":"10.1021\/acs.jproteome.3c00266","volume":"22","author":"C Homsi","year":"2023","unstructured":"Homsi C, Rajan RE, Minati R, St-Hilaire E, Bonneil E, Dufresne SF, Wurtele H, Verreault A, Thibault P (2023) A rapid and efficient method for the extraction of histone proteins. J Proteome Res 22:2765\u20132773. https:\/\/doi.org\/10.1021\/acs.jproteome.3c00266","journal-title":"J Proteome Res"},{"key":"4_CR28","doi-asserted-by":"publisher","unstructured":"Ledvinov\u00e1 D, Mikul\u00e1\u0161ek K, Kucha\u0159\u00edkov\u00e1 H, Brabencov\u00e1 S, Fojtov\u00e1 M, Zdr\u00e1hal Z, Lochmanov\u00e1 G (2018) Filter-aided sample preparation procedure for mass spectrometric analysis of plant histones. Front Plant Sci 9. https:\/\/doi.org\/10.3389\/fpls.2018.01373","DOI":"10.3389\/fpls.2018.01373"},{"key":"4_CR29","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.527","volume":"2","author":"R Scheid","year":"2022","unstructured":"Scheid R, Dowell JA, Sanders D, Jiang J, Denu JM, Zhong X (2022) Histone acid extraction and high throughput mass spectrometry to profile histone modifications in Arabidopsis thaliana. Curr Protoc 2:e527. https:\/\/doi.org\/10.1002\/cpz1.527","journal-title":"Curr Protoc"},{"key":"4_CR30","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/s13148-024-01710-1","volume":"16","author":"J Frohlich","year":"2024","unstructured":"Frohlich J, Liorni N, Mangoni M, Lochmanov\u00e1 G, P\u00edrek P, Ka\u0161t\u00e1nkov\u00e1 N, Pata P, Kucera J, Chaldakov GN, Tonchev AB, Pata I, Gorbunova V, Leire E, Zdr\u00e1hal Z, Mazza T, Vinciguerra M (2024) Epigenetic and transcriptional control of adipocyte function by centenarian-associated SIRT6 N308K\/A313S mutant. Clin Epigenetics 16:96. https:\/\/doi.org\/10.1186\/s13148-024-01710-1","journal-title":"Clin Epigenetics"},{"key":"4_CR31","doi-asserted-by":"publisher","first-page":"287","DOI":"10.3109\/19396368.2013.817626","volume":"59","author":"S Mao","year":"2013","unstructured":"Mao S, Goodrich RJ, Hauser R, Schrader SM, Chen Z, Krawetz SA (2013) Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling. Syst Biol Reprod Med 59:287\u2013295. https:\/\/doi.org\/10.3109\/19396368.2013.817626","journal-title":"Syst Biol Reprod Med"},{"key":"4_CR32","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/978-1-60327-461-6_16","volume":"464","author":"GR Green","year":"2009","unstructured":"Green GR, Do DP (2009) Purification and analysis of variant and modified histones using 2D PAGE. Methods Mol Biol 464:285\u2013302. https:\/\/doi.org\/10.1007\/978-1-60327-461-6_16","journal-title":"Methods Mol Biol"},{"key":"4_CR33","doi-asserted-by":"publisher","first-page":"8648","DOI":"10.1038\/ncomms9648","volume":"6","author":"N Abshiru","year":"2015","unstructured":"Abshiru N, Caron-Lizotte O, Rajan RE, Jamai A, Pomies C, Verreault A, Thibault P (2015) Discovery of protein acetylation patterns by deconvolution of peptide isomer mass spectra. Nat Commun 6:8648. https:\/\/doi.org\/10.1038\/ncomms9648","journal-title":"Nat Commun"},{"key":"4_CR34","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1038\/nprot.2016.057","volume":"11","author":"P Giansanti","year":"2016","unstructured":"Giansanti P, Tsiatsiani L, Low TY, Heck AJR (2016) Six alternative proteases for mass spectrometry\u2013based proteomics beyond trypsin. Nat Protoc 11:993\u20131006. https:\/\/doi.org\/10.1038\/nprot.2016.057","journal-title":"Nat Protoc"},{"key":"4_CR35","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/proteomes8030014","volume":"8","author":"EJ Dupree","year":"2020","unstructured":"Dupree EJ, Jayathirtha M, Yorkey H, Mihasan M, Petre BA, Darie CC (2020) A critical review of bottom-up proteomics: the good, the bad, and the future of this field. Proteomes 8:14. https:\/\/doi.org\/10.3390\/proteomes8030014","journal-title":"Proteomes"},{"key":"4_CR36","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1111\/febs.15707","volume":"289","author":"R Noberini","year":"2022","unstructured":"Noberini R, Robusti G, Bonaldi T (2022) Mass spectrometry-based characterization of histones in clinical samples: applications, progress, and challenges. FEBS J 289:1191\u20131213. https:\/\/doi.org\/10.1111\/febs.15707","journal-title":"FEBS J"},{"key":"4_CR37","doi-asserted-by":"publisher","first-page":"1148","DOI":"10.1074\/mcp.O114.046573","volume":"14","author":"TM Maile","year":"2015","unstructured":"Maile TM, Izrael-Tomasevic A, Cheung T, Guler GD, Tindell C, Masselot A, Liang J, Zhao F, Trojer P, Classon M, Arnott D (2015) Mass spectrometric quantification of histone post-translational modifications by a hybrid chemical labeling method. Mol Cell Proteomics 14:1148\u20131158. https:\/\/doi.org\/10.1074\/mcp.O114.046573","journal-title":"Mol Cell Proteomics"},{"key":"4_CR38","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1002\/pmic.201400483","volume":"15","author":"S Sidoli","year":"2015","unstructured":"Sidoli S, Yuan Z-F, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton L-M, Cao X-J, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, Garcia BA (2015) Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics 15:1459\u20131469. https:\/\/doi.org\/10.1002\/pmic.201400483","journal-title":"Proteomics"},{"key":"4_CR39","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1021\/ac303171h","volume":"85","author":"R Liao","year":"2013","unstructured":"Liao R, Wu H, Deng H, Yu Y, Hu M, Zhai H, Yang P, Zhou S, Yi W (2013) Specific and efficient N-propionylation of histones with propionic acid N-hydroxysuccinimide ester for histone marks characterization by LC-MS. Anal Chem 85:2253\u20132259. https:\/\/doi.org\/10.1021\/ac303171h","journal-title":"Anal Chem"},{"key":"4_CR40","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.aca.2015.06.019","volume":"886","author":"J Chen","year":"2015","unstructured":"Chen J, Gao J, Peng M, Wang Y, Yu Y, Yang P, Jin H (2015) In-gel NHS-propionate derivatization for histone post-translational modifications analysis in Arabidopsis thaliana. Anal Chim Acta 886:107\u2013113. https:\/\/doi.org\/10.1016\/j.aca.2015.06.019","journal-title":"Anal Chim Acta"},{"key":"4_CR41","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1167\/iovs.65.2.27","volume":"65","author":"MC Herwig-Carl","year":"2024","unstructured":"Herwig-Carl MC, Sharma A, Tischler V, Pelusi N, Loeffler KU, Holz FG, Zeschnigk M, Landreville S, Auw-Haedrich C, Noberini R, Bonaldi T (2024) Mass spectrometry-based profiling of histone post-translational modifications in uveal melanoma tissues, human melanocytes, and uveal melanoma cell lines\u2014a pilot study. Invest Ophthalmol Vis Sci 65:27. https:\/\/doi.org\/10.1167\/iovs.65.2.27","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"4_CR42","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1186\/s13148-021-01120-7","volume":"13","author":"R Noberini","year":"2021","unstructured":"Noberini R, Savoia EO, Brandini S, Greco F, Marra F, Bertalot G, Pruneri G, McDonnell LA, Bonaldi T (2021) Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clin Epigenetics 13:145. https:\/\/doi.org\/10.1186\/s13148-021-01120-7","journal-title":"Clin Epigenetics"},{"key":"4_CR43","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1074\/mcp.M900489-MCP200","volume":"9","author":"HR Jung","year":"2010","unstructured":"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\u2013850. https:\/\/doi.org\/10.1074\/mcp.M900489-MCP200","journal-title":"Mol Cell Proteomics"},{"key":"4_CR44","doi-asserted-by":"publisher","first-page":"2508","DOI":"10.1021\/jasms.3c00223","volume":"34","author":"RM Searfoss","year":"2023","unstructured":"Searfoss RM, Karki R, Lin Z, Robison F, Garcia BA (2023) An optimized and high-throughput method for histone propionylation and data-independent acquisition analysis for the identification and quantification of histone post-translational modifications. J Am Soc Mass Spectrom 34:2508\u20132517. https:\/\/doi.org\/10.1021\/jasms.3c00223","journal-title":"J Am Soc Mass Spectrom"},{"key":"4_CR45","doi-asserted-by":"publisher","first-page":"3252","DOI":"10.1021\/acs.jproteome.5b00245","volume":"14","author":"KA Krautkramer","year":"2015","unstructured":"Krautkramer KA, Reiter L, Denu JM, Dowell JA (2015) Quantification of SAHA-dependent changes in histone modifications using data-independent acquisition mass spectrometry. J Proteome Res 14:3252\u20133262. https:\/\/doi.org\/10.1021\/acs.jproteome.5b00245","journal-title":"J Proteome Res"},{"key":"4_CR46","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1002\/rcm.8401","volume":"33","author":"J Cole","year":"2019","unstructured":"Cole J, Hanson EJ, James DC, Dockrell DH, Dickman MJ (2019) Comparison of data-acquisition methods for the identification and quantification of histone post-translational modifications on a Q Exactive HF hybrid quadrupole Orbitrap mass spectrometer. Rapid Commun Mass Spectrom 33:897\u2013906. https:\/\/doi.org\/10.1002\/rcm.8401","journal-title":"Rapid Commun Mass Spectrom"},{"key":"4_CR47","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/nmeth1088","volume":"4","author":"AI Nesvizhskii","year":"2007","unstructured":"Nesvizhskii AI, Vitek O, Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787\u2013797. https:\/\/doi.org\/10.1038\/nmeth1088","journal-title":"Nat Methods"},{"key":"4_CR48","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","volume":"20","author":"DN Perkins","year":"1999","unstructured":"Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551\u20133567. https:\/\/doi.org\/10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","journal-title":"Electrophoresis"},{"key":"4_CR49","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","volume":"5","author":"JK Eng","year":"1994","unstructured":"Eng JK, McCormack AL, Yates JR (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\u2013989. https:\/\/doi.org\/10.1016\/1044-0305(94)80016-2","journal-title":"J Am Soc Mass Spectrom"},{"issue":"M111","key":"4_CR50","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M111.010587","volume":"11","author":"J Zhang","year":"2012","unstructured":"Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie GA, Ma B (2012) PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics 11(M111):010587. https:\/\/doi.org\/10.1074\/mcp.M111.010587","journal-title":"Mol Cell Proteomics"},{"key":"4_CR51","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.1074\/mcp.T600050-MCP200","volume":"6","author":"IV Shilov","year":"2007","unstructured":"Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA (2007) The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6:1638\u20131655. https:\/\/doi.org\/10.1074\/mcp.T600050-MCP200","journal-title":"Mol Cell Proteomics"},{"key":"4_CR52","doi-asserted-by":"publisher","first-page":"2985","DOI":"10.1002\/rcm.3173","volume":"21","author":"L-H Wang","year":"2007","unstructured":"Wang L-H, Li D-Q, Fu Y, Wang H-P, Zhang J-F, Yuan Z-F, Sun R-X, Zeng R, He S-M, Gao W (2007) pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry. Rapid Commun Mass Spectrom 21:2985\u20132991. https:\/\/doi.org\/10.1002\/rcm.3173","journal-title":"Rapid Commun Mass Spectrom"},{"key":"4_CR53","unstructured":"Andromeda: a peptide search engine integrated into the MaxQuant environment | Journal of Proteome Research. https:\/\/pubs.acs.org\/doi\/10.1021\/pr101065j. Accessed 23 Jul 2025"},{"key":"4_CR54","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1021\/pr0499491","volume":"3","author":"LY Geer","year":"2004","unstructured":"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\u2013964. https:\/\/doi.org\/10.1021\/pr0499491","journal-title":"J Proteome Res"},{"key":"4_CR55","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1021\/ac0258709","volume":"75","author":"D Feny\u00f6","year":"2003","unstructured":"Feny\u00f6 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\u2013774. https:\/\/doi.org\/10.1021\/ac0258709","journal-title":"Anal Chem"},{"key":"4_CR56","doi-asserted-by":"publisher","first-page":"4470","DOI":"10.1021\/pr5008015","volume":"13","author":"Z-F Yuan","year":"2014","unstructured":"Yuan Z-F, Lin S, Molden RC, Garcia BA (2014) Evaluation of proteomic search engines for the analysis of histone modifications. J Proteome Res 13:4470\u20134478. https:\/\/doi.org\/10.1021\/pr5008015","journal-title":"J Proteome Res"},{"key":"4_CR57","doi-asserted-by":"publisher","first-page":"2084","DOI":"10.3389\/fpls.2017.02084","volume":"8","author":"S Brabencov\u00e1","year":"2017","unstructured":"Brabencov\u00e1 S, Ihnatov\u00e1 I, Pot\u011b\u0161il D, Fojtov\u00e1 M, Fajkus J, Zdr\u00e1hal Z, Lochmanov\u00e1 G (2017) Variations of histone modification patterns: contributions of inter-plant variability and technical factors. Front Plant Sci 8:2084. https:\/\/doi.org\/10.3389\/fpls.2017.02084","journal-title":"Front Plant Sci"},{"key":"4_CR58","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcpro.2024.100795","volume":"23","author":"M Franek","year":"2024","unstructured":"Franek M, Ne\u0161por Dadejov\u00e1 M, P\u00edrek P, Kry\u0161tofov\u00e1 K, Dobisov\u00e1 T, Zdr\u00e1hal Z, Dvo\u0159\u00e1\u010dkov\u00e1 M, Lochmanov\u00e1 G (2024) Histone chaperone deficiency in Arabidopsis plants triggers adaptive epigenetic changes in histone variants and modifications. Mol Cell Proteomics 23:100795. https:\/\/doi.org\/10.1016\/j.mcpro.2024.100795","journal-title":"Mol Cell Proteomics"},{"key":"4_CR59","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1111\/tpj.15145","volume":"106","author":"K Kol\u00e1\u0159ov\u00e1","year":"2021","unstructured":"Kol\u00e1\u0159ov\u00e1 K, Ne\u0161por Dadejov\u00e1 M, Loja T, Lochmanov\u00e1 G, S\u00fdkorov\u00e1 E, Dvo\u0159\u00e1\u010dkov\u00e1 M (2021) Disruption of NAP1 genes in Arabidopsis thaliana suppresses the fas1 mutant phenotype, enhances genome stability and changes chromatin compaction. Plant J 106:56\u201373. https:\/\/doi.org\/10.1111\/tpj.15145","journal-title":"Plant J"},{"key":"4_CR60","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","volume":"26","author":"B MacLean","year":"2010","unstructured":"MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26:966\u2013968. https:\/\/doi.org\/10.1093\/bioinformatics\/btq054","journal-title":"Bioinformatics"},{"key":"4_CR61","doi-asserted-by":"publisher","first-page":"2533","DOI":"10.1021\/acs.jproteome.8b00133","volume":"17","author":"Z-F Yuan","year":"2018","unstructured":"Yuan Z-F, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA (2018) EpiProfile 2.0: a computational platform for processing epi-proteomics mass spectrometry data. J Proteome Res 17:2533\u20132541. https:\/\/doi.org\/10.1021\/acs.jproteome.8b00133","journal-title":"J Proteome Res"},{"key":"4_CR62","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.1002\/pmic.201100033","volume":"11","author":"Y Levin","year":"2011","unstructured":"Levin Y (2011) The role of statistical power analysis in quantitative proteomics. Proteomics 11:2565\u20132567. https:\/\/doi.org\/10.1002\/pmic.201100033","journal-title":"Proteomics"},{"key":"4_CR63","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1021\/acs.jproteome.6b00645","volume":"16","author":"MR Al Shweiki","year":"2017","unstructured":"Al Shweiki MR, M\u00f6nchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W (2017) Assessment of label-free quantification in discovery proteomics and impact of technological factors and natural variability of protein abundance. J Proteome Res 16:1410\u20131424. https:\/\/doi.org\/10.1021\/acs.jproteome.6b00645","journal-title":"J Proteome Res"},{"key":"4_CR64","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1111\/j.2517-6161.1982.tb01195.x","volume":"44","author":"J Aitchison","year":"1982","unstructured":"Aitchison J (1982) The statistical analysis of compositional data. J R Stat Soc Ser B (Methodol) 44:139\u2013160. https:\/\/doi.org\/10.1111\/j.2517-6161.1982.tb01195.x","journal-title":"J R Stat Soc Ser B (Methodol)"},{"key":"4_CR65","doi-asserted-by":"publisher","first-page":"3095","DOI":"10.1016\/j.csda.2009.11.023","volume":"54","author":"K Hron","year":"2010","unstructured":"Hron K, Templ M, Filzmoser P (2010) Imputation of missing values for compositional data using classical and robust methods. Comput Stat Data Anal 54:3095\u20133107. https:\/\/doi.org\/10.1016\/j.csda.2009.11.023","journal-title":"Comput Stat Data Anal"},{"key":"4_CR66","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1016\/j.fertnstert.2009.09.009","volume":"92","author":"F Zegers-Hochschild","year":"2009","unstructured":"Zegers-Hochschild F, Adamson GD, de Mouzon J, Ishihara O, Mansour R, Nygren K, Sullivan E, Vanderpoel S, International Committee for Monitoring Assisted Reproductive Technology, World Health Organization (2009) International Committee for Monitoring Assisted Reproductive Technology (ICMART) and the World Health Organization (WHO) revised glossary of ART terminology, 2009. Fertil Steril 92:1520\u20131524. https:\/\/doi.org\/10.1016\/j.fertnstert.2009.09.009","journal-title":"Fertil Steril"},{"key":"4_CR67","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.ecl.2007.03.012","volume":"36","author":"JP Jarow","year":"2007","unstructured":"Jarow JP (2007) Diagnostic approach to the infertile male patient. Endocrinol Metab Clin N Am 36:297\u2013311. https:\/\/doi.org\/10.1016\/j.ecl.2007.03.012","journal-title":"Endocrinol Metab Clin N Am"},{"key":"4_CR68","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1590\/s1807-59322011000400026","volume":"66","author":"SC Esteves","year":"2011","unstructured":"Esteves SC, Miyaoka R, Agarwal A (2011) An update on the clinical assessment of the infertile male. [corrected]. Clinics (Sao Paulo) 66:691\u2013700. https:\/\/doi.org\/10.1590\/s1807-59322011000400026","journal-title":"Clinics (Sao Paulo)"},{"key":"4_CR69","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1590\/s1677-55382012000500002","volume":"38","author":"A Hamada","year":"2012","unstructured":"Hamada A, Esteves SC, Nizza M, Agarwal A (2012) Unexplained male infertility: diagnosis and management. Int Braz J Urol 38:576\u2013594. https:\/\/doi.org\/10.1590\/s1677-55382012000500002","journal-title":"Int Braz J Urol"},{"key":"4_CR70","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s13596-017-0269-7","volume":"17","author":"M Naz","year":"2017","unstructured":"Naz M, Kamal M (2017) Classification, causes, diagnosis and treatment of male infertility: a review. Orient Pharm Exp Med 17:89\u2013109. https:\/\/doi.org\/10.1007\/s13596-017-0269-7","journal-title":"Orient Pharm Exp Med"},{"key":"4_CR71","doi-asserted-by":"publisher","first-page":"62","DOI":"10.23750\/abm.v90i10-S.8762","volume":"90","author":"G Guerri","year":"2019","unstructured":"Guerri G, Maniscalchi T, Barati S, Busetto GM, Del Giudice F, De Berardinis E, Cannarella R, Calogero AE, Bertelli M (2019) Non-syndromic monogenic male infertility. Acta Bio Medica Atenei Parmensis 90:62\u201367. https:\/\/doi.org\/10.23750\/abm.v90i10-S.8762","journal-title":"Acta Bio Medica Atenei Parmensis"},{"key":"4_CR72","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/humupd\/dmab030","volume":"28","author":"BJ Houston","year":"2021","unstructured":"Houston BJ, Riera-Escamilla A, Wyrwoll MJ, Salas-Huetos A, Xavier MJ, Nagirnaja L, Friedrich C, Conrad DF, Aston KI, Krausz C, T\u00fcttelmann F, O\u2019Bryan MK, Veltman JA, Oud MS (2021) A systematic review of the validated monogenic causes of human male infertility: 2020 update and a discussion of emerging gene-disease relationships. Hum Reprod Update 28:15\u201329. https:\/\/doi.org\/10.1093\/humupd\/dmab030","journal-title":"Hum Reprod Update"}],"container-title":["Advances in Experimental Medicine and Biology","Emerging Sample Treatments in Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-032-21638-0_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T22:53:24Z","timestamp":1783205604000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-032-21638-0_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9783032216373","9783032216380"],"references-count":72,"URL":"https:\/\/doi.org\/10.1007\/978-3-032-21638-0_4","relation":{},"ISSN":["0065-2598","2214-8019"],"issn-type":[{"value":"0065-2598","type":"print"},{"value":"2214-8019","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"2 June 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}