PXD010981 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Quantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments |
Description | The 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. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_04:07:54.852.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD010981 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Yasset Perez-Riverol |
SpeciesList | scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | Oxidation; Carbamidomethyl |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-09-03 02:31:39 | ID requested | |
1 | 2018-09-10 02:08:35 | announced | |
2 | 2018-12-04 04:07:31 | announced | Updated project metadata. |
⏵ 3 | 2024-10-22 04:08:00 | announced | 2024-10-22: 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 affiliation | Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen,Germany |
contact email | sachsenb@informatik.uni-tuebingen.de |
lab head | |
Yasset Perez-Riverol |
contact affiliation | EBI |
contact email | yperez@ebi.ac.uk |
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/2018/09/PXD010981 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD010981
- Label: PRIDE project
- Name: Quantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments