PXD002885

PXD002885 is an original dataset announced via ProteomeXchange.

Title	Histone datasets for evaluation of histone extraction protocols
Description	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.
HostingRepository	PRIDE
AnnounceDate	2016-10-11
AnnouncementXML	Submission_2016-10-11_02:04:11.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Elisabeth Govaert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; amidated residue; trimethylated residue; phosphorylated residue; acetylated residue; dimethylated residue; propanoylated residue; butanoylated residue
Instrument	Synapt G2-S HDMS

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-10 01:27:18	ID requested
⏵ 1	2016-10-11 02:04:12	announced

Govaert E, Van Steendam K, Scheerlinck E, Vossaert L, Meert P, Stella M, Willems S, De Clerck L, Dhaenens M, Deforce D, Extracting histones for the specific purpose of label-free MS. Proteomics, 16(23):2937-2944(2016) [pubmed]

curator keyword: Technical

submitter keyword: histone, extraction protocols, label-free MS, targeted and untargeted analysis

Dieter Deforce
contact affiliation	Faculty of Pharmaceutical Sciences, Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Belgium
contact email	Dieter.Deforce@UGent.be
lab head
Elisabeth Govaert
contact affiliation	Ghent University
contact email	Elisabeth.Govaert@UGent.be
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/2016/10/PXD002885

PRIDE project URI

• PRIDE
  1. PXD002885
     1. Label: PRIDE project
     2. Name: Histone datasets for evaluation of histone extraction protocols