PXD001240

PXD001240 is an original dataset announced via ProteomeXchange.

Title	Benchmarking label-free quantification based on data-independent acquisition (DIA) workflows
Description	Label-free quantification based on data-independent acquisition (DIA) workflows is increasingly popular. Several software tools have been recently published or are commercially available. The present study focuses on the critical evaluation of three different software packages (Progenesis, synapter and ISOQuant) supporting ion-mobility enhanced DIA data. In order to benchmark the label-free quantification performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, E.coli). This model data set simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and down-regulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on the variation of reported protein quantities between technical replicates.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:02:55.092.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stefan Tenzer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	deaminated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2014-08-15 01:51:28	ID requested
1	2015-01-07 04:59:11	announced
2	2017-04-11 00:28:14	announced	Updated project metadata.
⏵ 3	2024-10-22 04:02:57	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201400396;

Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S, In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics, 15(18):3140-51(2015) [pubmed]

curator keyword: Technical

submitter keyword: Human, Yeast, E.coli

Stefan Tenzer
contact affiliation	University Medical Center Mainz, Institute for Immunology
contact email	tenzer@uni-mainz.de
lab head
Stefan Tenzer
contact affiliation	Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
contact email	tenzer@uni-mainz.de
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/2017/04/PXD001240

PRIDE project URI

• PRIDE
  1. PXD001240
     1. Label: PRIDE project
     2. Name: Benchmarking label-free quantification based on data-independent acquisition (DIA) workflows