PXD002099

PXD002099 is an original dataset announced via ProteomeXchange.

Title	Optimization of statistical methods impact on quantitative proteomics data
Description	As tools for quantitative label-free mass spectrometry (MS) rapidly develop a consensus about the best practices is not apparent. In the work described here we compared five popular statistical methods for detecting differential protein expression from quantitative MS data using both controlled experiments with known quantitative differences for specific proteins used as standards, as well as ‘real’ experiments where differences in protein abundance are not known a priori. Our results suggest that data-driven reproducibility-optimization can consistently produce reliable differential expression rankings for label-free proteome tools and are straightforward in their application.
HostingRepository	PRIDE
AnnounceDate	2015-09-03
AnnouncementXML	Submission_2015-09-03_02:56:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anni Vehmas
SpeciesList	scientific name: Candida albicans (Yeast); NCBI TaxID: 5476;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-24 02:24:12	ID requested
⏵ 1	2015-09-03 02:56:31	announced

Pursiheimo A, Vehmas AP, Afzal S, Suomi T, Chand T, Strauss L, Poutanen M, Rokka A, Corthals GL, Elo LL, Optimization of Statistical Methods Impact on Quantitative Proteomics Data. J Proteome Res, 14(10):4118-26(2015) [pubmed]

curator keyword: Technical

submitter keyword: proteomics, label-free mass spectrometry, quantitative analysis, statistical methods, reproducibility, ROTS

Laura L. Elo
contact affiliation	Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland; Department of Mathematics and Statistics, FI-20014, University of Turku, Finland
contact email	laliel@utu.fi
lab head
Anni Vehmas
contact affiliation	Turku Centre for Biotechnology, University of Turku and Åbo Akademi University
contact email	avehmas@btk.fi
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/2015/09/PXD002099

PRIDE project URI

• PRIDE
  1. PXD002099
     1. Label: PRIDE project
     2. Name: Optimization of statistical methods impact on quantitative proteomics data