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Multiplexed data independent acquisition (MSX‐DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides
Author(s) -
Sidoli Simone,
Fujiwara Rina,
Garcia Benjamin A.
Publication year - 2016
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201500527
Subject(s) - mass spectrometry , histone , proteomics , chemistry , multiplexing , quantitative proteomics , isobaric labeling , chromatography , tandem mass spectrometry , computer science , biochemistry , dna , protein mass spectrometry , telecommunications , gene
We present the MS‐based application of the innovative, although scarcely exploited, multiplexed data‐independent acquisition (MSX‐DIA) for the analysis of histone PTMs. Histones are golden standard for complexity in MS based proteomics, due to their large number of combinatorial modifications, leading to isobaric peptides after proteolytic digestion. DIA has, thus, gained popularity for the purpose as it allows for MS/MS‐based quantification without upfront assay development. In this work, we evaluated the performance of traditional DIA versus MSX‐DIA in terms of MS/MS spectra quality, instrument scan rate and quantification precision using histones from HeLa cells. We used an MS/MS isolation window of 10 and 6 m/z for DIA and MSX‐DIA, respectively. Four MS/MS scans were multiplexed for MSX‐DIA. Despite MSX‐DIA was programmed to perform two‐fold more MS/MS events than traditional DIA, it acquired on average ∼5% more full MS scans, indicating even faster scan rate. Results highlighted an overall decrease of background ion signals using MSX‐DIA, and we illustrated specific examples where peptides of different precursor masses were co‐fragmented by DIA but not MSX‐DIA. Taken together, MSX‐DIA proved thus to be a more favorable method for histone analysis in data independent mode.