PXD006190

PXD006190 is an original dataset announced via ProteomeXchange.

Title	Comparison of fractionation proteomics for local SWATH library building
Description	For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells.
HostingRepository	PRIDE
AnnounceDate	2017-07-04
AnnouncementXML	Submission_2017-07-04_07:03:06.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	methylthiolated residue; monohydroxylated residue; deamidated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-28 01:27:12	ID requested
⏵ 1	2017-07-04 07:03:07	announced

Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D, Comparison of fractionation proteomics for local SWATH library building. Proteomics, 17(15-16):(2017) [pubmed]

curator keyword: Technical

submitter keyword: comparative study, fractionation proteomics, hESC, library building, SWATH-MS

Prof. Dr. Apr. Dieter Deforce
contact affiliation	Laboratory of Pharmaceutical Biotechnology, Ghent University, Faculty of Pharmaceutical Sciences, Ottergemsesteenweg 460, 9000 Ghent, 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/2017/07/PXD006190

PRIDE project URI

• PRIDE
  1. PXD006190
     1. Label: PRIDE project
     2. Name: Comparison of fractionation proteomics for local SWATH library building