PXD002952-2

PXD002952 is an original dataset announced via ProteomeXchange.

Title	LFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
Description	The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, Spectronaut, DIA-Umpire, in collaboration with the respective developers to ensure an optimal use of each tool. We analyzed data from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments applying different SWATH isolation windows setups. Using the resulting high-complexity datasets we benchmarked precision and accuracy of quantification and evaluated identification performance, robustness and specificity of each software tool. To consistently evaluate the high complexity datasets, we developed the LFQbench R-package. LFQbench results enabled developers to improve their software tools, thereby underlining the value of the reference datasets for software development and benchmarking. All tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.
HostingRepository	PRIDE
AnnounceDate	2016-09-28
AnnouncementXML	Submission_2018-04-04_03:57:44.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yasset Perez-Riverol
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	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-21 07:59:44	ID requested
1	2016-09-27 16:18:43	announced
⏵ 2	2018-04-04 03:57:45	announced	Updated publication reference for PubMed record(s): 27701404.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, R, ö, st HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S, A multicenter study benchmarks software tools for label-free proteome quantification. Nat Biotechnol, 34(11):1130-1136(2016) [pubmed]

submitter keyword: SWATH-MS, LFQ, Benchmark, LFQbench

Stefan Tenzer
contact affiliation	Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
contact email	tenzer@uni-mainz.de
lab head
Yasset Perez-Riverol
contact affiliation	EBI
contact email	yperez@ebi.ac.uk
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/2016/09/PXD002952

PRIDE project URI

• PRIDE
  1. PXD002952
     1. Label: PRIDE project
     2. Name: LFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification