PXD044981

PXD044981 is an original dataset announced via ProteomeXchange.

Title	Benchmarking DIA data analysis workflows
Description	Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows through a ground truth sample mimicking real differential abundance samples, consisting of a differential spike-in of UPS2 in a constant yeast background, we provide a roadmap for DIA data analysis of shotgun samples based on whether sensitivity, precision or accuracy is of the essence. Three different commonly used DIA software tools (DIA-NN, EncyclopeDIA and SpectronautTM) were tested in both spectral library mode and spectral library free mode. In spectral library mode we used the independent spectral library prediction tools Prosit and MS2PIP together with DeepLC, next to the classical DDA-based spectral libraries. In total we benchmarked 12 DIA workflows. DIA-NN in library free mode or using in silico predicted libraries shows the highest sensitivity maintaining a high reproducibility and accuracy.
HostingRepository	PRIDE
AnnounceDate	2024-05-06
AnnouncementXML	Submission_2024-05-06_04:28:53.337.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	An Staes
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-30 16:09:23	ID requested
⏵ 1	2024-05-06 04:28:54	announced

10.1021/ACS.JPROTEOME.4C00048;

submitter keyword: shotgun proteomics, in silico library, LC-MS, DDA library, Data analysis, benchmark,DIA, library free

Simon Devos
contact affiliation	1)VIB Center for Medical Biotechnology, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium 2)Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium 3)VIB Proteomics Core, Technologiepark-Zwijnaarde 75, B9052 Ghent, Belgium
contact email	Simon.devos@vib-ugent.be
lab head
An Staes
contact affiliation	Medical Protein Chemistry
contact email	an.staes@vib-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/2024/05/PXD044981

PRIDE project URI

• PRIDE
  1. PXD044981
     1. Label: PRIDE project
     2. Name: Benchmarking DIA data analysis workflows