2021
DOI: 10.3390/proteomes9020017
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Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions

Abstract: Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation … Show more

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Cited by 8 publications
(11 citation statements)
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“…S2 (ESI †) displays the coverage plots of the hPTMs on H3.1 and H4 detected by the three Mascot searches, color coded according to the number of spectra covering this residue, as presented recently elsewhere. 34 In the standard search, 1309 PSMs were found with an Nterminal fixed propionylation, comprising a total of 596 PSMs with acetylation. From the targeted precursor ion population (171 precursor ions), 18 precursor ions got annotated in this standard search (Fig.…”
Section: Resultsmentioning
confidence: 99%
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“…S2 (ESI †) displays the coverage plots of the hPTMs on H3.1 and H4 detected by the three Mascot searches, color coded according to the number of spectra covering this residue, as presented recently elsewhere. 34 In the standard search, 1309 PSMs were found with an Nterminal fixed propionylation, comprising a total of 596 PSMs with acetylation. From the targeted precursor ion population (171 precursor ions), 18 precursor ions got annotated in this standard search (Fig.…”
Section: Resultsmentioning
confidence: 99%
“…First, the search parameters were adapted to search for chemical noise derived from derivatization using propionic anhydride. 29,30,34,[36][37][38] Therefore, the data was re-searched by setting propionylation at N-terminus and at K as variable modifications (to assess underpropionylation) and by including variable formylation at STYK to detect (spontaneously) induced formylation (sample preparation search; Table 1). 34,39 596 spectra were annotated with a formylation, giving rise to one additional annotation of the declining ion population because they also carried an acetylation (Fig.…”
Section: Resultsmentioning
confidence: 99%
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