PXD011198

PXD011198 is an original dataset announced via ProteomeXchange.

Title	hSWATH: Unlocking SWATH’s full potential for an untargeted histone perspective
Description	Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of a time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e. acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.
HostingRepository	PRIDE
AnnounceDate	2019-08-27
AnnouncementXML	Submission_2019-08-27_05:47:04.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011198
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Maarten Dhaenens
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	EG Propionyl
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-27 02:29:51	ID requested
⏵ 1	2019-08-27 05:47:05	announced

De Clerck L, Willems S, Noberini R, Restellini C, Van Puyvelde B, Daled S, Bonaldi T, Deforce D, Dhaenens M, hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective. J Proteome Res, 18(11):3840-3849(2019) [pubmed]

submitter keyword: Sequential window acquisition of all theoretical fragment ion spectra (SWATH)

Data independent acquisition (DIA)

Histone

Mass spectrometry (MS)

Post-translational modification (PTM)

Epigenetics

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
contact email	maarten.Dhaenens@ugent.be
lab head
Maarten Dhaenens
contact affiliation	Faculity of Pharmaceutical Biotechnology
contact email	maarten.dhaenens@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/2019/08/PXD011198

PRIDE project URI

• PRIDE
  1. PXD011198
     1. Label: PRIDE project
     2. Name: hSWATH: Unlocking SWATH’s full potential for an untargeted histone perspective