Proteomics

Dataset Information

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Histone datasets for evaluation of histone extraction protocols

ABSTRACT: Extracting histones from cells is a routine operation for studies that aim to characterize histones and their post-translational modifications (hPTMs). However, label-free quantitative mass spectrometry (MS) approaches, both data-dependent (DDA) and data-independent (DIA), require streamlined protocols that are highly reproducible even at the peptide level, to enable simultaneous accurate quantification of dozens to hundreds of these hPTMs. We present a step-by-step comparison of different histone extraction protocols based on literature and evaluate their suitability for label-free MS purposes using a nanoESI label-free MS1 intensity-based DDA MS experiment. We evaluate the data both using a targeted and an untargeted (Progenesis QI) approach.

INSTRUMENT(S): Synapt G2-S HDMS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture, T Cell

DISEASE(S): Acute Leukemia

SUBMITTER: Elisabeth Govaert  

LAB HEAD: Dieter Deforce

PROVIDER: PXD002885 | Pride | 2016-10-11

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
ProgenesisAnalysis.zip Other
Rawdata.zip Other
Searchstrategy_custom-madeDB_allMSMSspectra.mgf Mgf
Searchstrategy_custommadeDB.dat Other
Targetedanalysis.dat Other
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Publications

Extracting histones from cells is the first step in studies that aim to characterize histones and their post-translational modifications (hPTMs) with MS. In the last decade, label-free quantification is more frequently being used for MS-based histone characterization. However, many histone extraction protocols were not specifically designed for label-free MS. While label-free quantification has its advantages, it is also very susceptible to technical variation. Here, we adjust an established his  ...[more]

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