PXD010981

PXD010981 is an original dataset announced via ProteomeXchange.

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

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.

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]

curator keyword: Technical, Biological

submitter keyword: OpenMS, Label-free,Benchmark, IPRG2015, IPRG Study, Reference Dataset

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

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

• PRIDE
  1. PXD010981
     1. Label: PRIDE project
     2. Name: Quantitation Analysis using OpenMS of iPRG2015: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments