PXD004166

PXD004166 is an original dataset announced via ProteomeXchange.

Title	EpiProfile 2.0: a proteomics tool to quantify histone modifications by mass spectrometry
Description	The histone LC-MS/MS data analysis is challenging due to the large number and variety of isobaric histone peptides, and the high dynamic range of histone peptide abundances. We introduce EpiProfile 2.0 to quantify histone post-translational modifications from mass spectrometry data, in which fragment ions are used to determine the retention time of peptides and discriminate isobaric peptides. EpiProfile can automatically recognize and efficiently process both data-dependent and data-independent acquisition runs (DDA and DIA), and high-resolution and low-resolution instrument runs. The proteomics tool was tested on human cells and validated by synthetic histone peptides. EpiProfile is the first automatic program to determine the retention time and discriminate isobaric peptides for histone modifications with DIA MS.
HostingRepository	PRIDE
AnnounceDate	2018-05-29
AnnouncementXML	Submission_2018-05-29_07:40:51.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004166
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	phosphorylated residue; acetylated residue; formylated residue; propanoylated residue; butanoylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-17 06:44:47	ID requested
⏵ 1	2018-05-29 07:40:52	announced

Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA, EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. J Proteome Res, 17(7):2533-2541(2018) [pubmed]

curator keyword: Technical, Biological

submitter keyword: histone, post-translational modification, proteomics, quantification, mass spectrometry

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD004166

PRIDE project URI

• PRIDE
  1. PXD004166
     1. Label: PRIDE project
     2. Name: EpiProfile 2.0: a proteomics tool to quantify histone modifications by mass spectrometry