PXD013231-3

PXD013231 is an original dataset announced via ProteomeXchange.

Title	Analysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance
Description	Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies (1, 2), we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined a optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform is capable of measuring 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1,508 samples.
HostingRepository	PRIDE
AnnounceDate	2019-04-11
AnnouncementXML	Submission_2019-05-14_07:22:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roland Bruderer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-26 00:46:29	ID requested
1	2019-04-06 00:30:10	announced
2	2019-04-11 00:31:11	announced	Updated project metadata.
⏵ 3	2019-05-14 07:22:35	announced	Updated project metadata.
4	2024-10-22 04:03:07	announced	2024-10-22: Updated project metadata.

Bruderer R, Muntel J, M, ü, ller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L, Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance. Mol Cell Proteomics, 18(6):1242-1254(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: plasma proteomics, data-independent acquisition, SWATH, label-free quantification, stable isotope-based quantification, library, single shot, high throughput, clinical proteomics

Lukas Reiter
contact affiliation	Biognosys AG, Schlieren, Schweiz
contact email	lukas.reiter@biognosys.ch
lab head
Roland Bruderer
contact affiliation	Biognosys AG
contact email	roland.bruderer@biognosys.com
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/2019/04/PXD013231

PRIDE project URI

• PRIDE
  1. PXD013231
     1. Label: PRIDE project
     2. Name: Analysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance