PXD001541

PXD001541 is an original dataset announced via ProteomeXchange.

Title	Quantifying histone PTMs by bottom-up MS
Description	Histone post-translational modifications (PTMs) contribute to chromatin function through their chemical properties which influence chromatin structure, and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis due to the high sensitivity and the high mass accuracy that provide confident identification. However, the histone nanoLC-MS/MS data analysis is even more challenging due to the large number and variety of isobaric histone peptides, and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to label-free quantification of histone peptides, EpiProfile is flexible, and can quantify different types of isotopically labeled histone peptides. EpiProfile is much more convenient when compared to manual quantification, filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoLC-MS/MS based quantification tool for histone modifications, which can also be adapted to analyze non-histone protein samples.
HostingRepository	PRIDE
AnnounceDate	2015-03-27
AnnouncementXML	Submission_2015-03-27_03:04:11.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001541
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Zuo-Fei Yuan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	butanoylated residue; acetylated residue; phosphorylated residue; propanoylated residue; formylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-26 01:27:56	ID requested
⏵ 1	2015-03-27 03:04:12	announced

Yuan ZF, Lin S, Molden RC, Cao XJ, Bhanu NV, Wang X, Sidoli S, Liu S, Garcia BA, EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra. Mol Cell Proteomics, 14(6):1696-707(2015) [pubmed]

curator keyword: Biological

submitter keyword: histone, post-translational modification, proteomics, quantification, retention time, isobaric peptide

Benjamin A. Garcia
contact affiliation	Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania
contact email	bgarci@mail.med.upenn.edu
lab head
Zuo-Fei Yuan
contact affiliation	UPenn
contact email	zuoyuan@mail.med.upenn.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001541
     1. Label: PRIDE project
     2. Name: Quantifying histone PTMs by bottom-up MS