<<< Full experiment listing


PXD001240 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBenchmarking label-free quantification based on data-independent acquisition (DIA) workflows
DescriptionLabel-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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterStefan 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;
ModificationListmonohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
InstrumentSynapt MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-08-15 01:51:28ID requested
12015-01-07 04:59:11announced
22017-04-11 00:28:14announcedUpdated project metadata.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: Human, Yeast, E.coli
Contact List
Stefan Tenzer
contact affiliationUniversity Medical Center Mainz, Institute for Immunology
contact emailtenzer@uni-mainz.de
lab head
Stefan Tenzer
contact affiliationInstitute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
contact emailtenzer@uni-mainz.de
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]