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PXD002952 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLFQbench enables a multi-centered benchmark study demonstrating robust proteomic label-free quantification
DescriptionThe 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterYasset 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;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-09-21 07:59:44ID requested
12016-09-27 16:18:43announced
22018-04-04 03:57:45announcedUpdated publication reference for PubMed record(s): 27701404.
Publication List
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, R, รถ, 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]
Keyword List
submitter keyword: SWATH-MS, LFQ, Benchmark, LFQbench
Contact List
Stefan Tenzer
contact affiliationInstitute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
contact emailtenzer@uni-mainz.de
lab head
Yasset Perez-Riverol
contact affiliationEBI
contact emailyperez@ebi.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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