ArticleRapid communications in mass spectrometry : RCM2019
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.
Article in Rapid communications in mass spectrometry : RCM, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Proteomic Analysis of Histone Sequence Variants and Post-translationally Modified Forms.Advances in experimental medicine and biology · 2026Review
- Breaking Boundaries in Histone Modification MS-Based Detection: A Tailored Search Strategy for Unrestricted Identification of Novel Epigenetic Marks.Molecular & cellular proteomics : MCP · 2025Article
- Arg-C Ultra Simplifies Histone Preparation for LC-MS/MS.Analytical chemistry · 2025Article
- A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.Genome biology · 2025Article
- An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.Journal of the American Society for Mass Spectrometry · 2023Article
- Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803.Photosynthesis research · 2023Article
- Insight on physicochemical properties governing peptide MS1 response in HPLC-ESI-MS/MS: A deep learning approach.Computational and structural biotechnology journal · 2023Article
- Glycosylation Analysis of Feline Small Intestine FollowingAnimals : an open access journal from MDPI · 2022Article
- Evaluation of acquisition modes for semi-quantitative analysis by targeted and untargeted mass spectrometry.Rapid communications in mass spectrometry : RCM · 2022Article
- Pneumolysin Is Responsible for Differential Gene Expression and Modifications in the Epigenetic Landscape of Primary Monocyte Derived Macrophages.Frontiers in immunology · 2021Article
- 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 communications in mass spectrometry : RCM · 2019Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
rationaleHistone post-translational modifications (PTMs) play key roles in regulating eukaryotic gene expression. Mass spectrometry (MS) has emerged as a powerful method to characterize and quantify histone PTMs as it allows unbiased identification and quantification of multiple histone PTMs including combinations of the modifications present.
methodsIn this study we compared a range of data-acquisition methods for the identification and quantification of the histone PTMs using a Q Exactive HF Orbitrap. We compared three different data-dependent analysis (DDA) methods with MS2 resolutions of 120K, 60K, 30K. We also compared a range of data-independent analysis (DIA) methods using MS2 isolation windows of 20 m/z and DIAvw to identify and quantify histone PTMs in Chinese hamster ovary (CHO) cells.
resultsThe increased number of MS2 scans afforded by the lower resolution methods resulted in a higher number of queries, peptide sequence matches (PSMs) and a higher number of peptide proteoforms identified with a Mascot Ion score greater than 46. No difference in the proportion of peptide proteoforms with Delta scores >17 was observed. Lower coefficients of variation (CVs) were obtained in the DIA MS1 60 K MS2 30 K 20 m/z isolation windows compared with the other data-acquisition methods.
conclusionsWe observed that DIA which offers advantages in flexibility and identification of isobaric peptide proteoforms performs as well as DDA in the analysis of histone PTMs. We were able to identify 71 modified histone peptides for histone H3 and H4 and quantified 64 across each of the different acquisition methods.
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