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PXD010981

PXD010981 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments
DescriptionThe 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC–tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts’ expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available. This project contains the analysis performed with OpenMS framework and exported to mztab. This is the first official submission of mzTab (PRIDE Complete Submission) and should used as reference by software providers as example of How to export Quantitative results into PRIDE database as Complete submission.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:07:54.852.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD010981
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterYasset Perez-Riverol
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListOxidation; Carbamidomethyl
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-09-03 02:31:39ID requested
12018-09-10 02:08:35announced
22018-12-04 04:07:31announcedUpdated project metadata.
32024-10-22 04:08:00announced2024-10-22: Updated project metadata.
Publication List
10.1021/acs.jproteome.6b00881;
10.6019/PXD010981;
Choi M, Eren-Dogu ZF, Colangelo C, Cottrell J, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments. J Proteome Res, 16(2):945-957(2017) [pubmed]
Keyword List
curator keyword: Technical, Biological
submitter keyword: OpenMS, Label-free,Benchmark, IPRG2015, IPRG Study, Reference Dataset
Contact List
Timo Sachsenberg
contact affiliationApplied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen,Germany
contact emailsachsenb@informatik.uni-tuebingen.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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