PXD004025

PXD004025 is an original dataset announced via ProteomeXchange.

Title	Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance
Description	Proteome wide protein quantification has become facile in the last years supported by label-free discovery proteomics approaches and powerful, easy to use software. We set out to independently evaluate this highly peptide centric technology focusing on the performance of some of the currently most popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant and Progenesis QIP. The sample to sample variability introduced into protein abundance estimates by the technology itself, thereby affecting the validity of changes in protein abundance reported to be biological in nature, was determined. Using the same experimental design we were interested in the potential of shotgun proteomics to uncover biological contributions to changes in protein abundance in essentially isogenic plants grown under the same environmental conditions. The accuracy, precision, limit of quantification, intra-analysis repeatability and other performance metrics of protein quantification were determined with the softwares’ ready-to-run, default parameters and some modified settings. MaxQuant and Progenesis QIP each had decided advantages and exhibited direct proportionality between measured and actual protein abundance. The inherent variability in protein quantification in measurements of Arabidopsis thaliana proteomes was substantially higher than the biological sample to sample variability. Strikingly, correlation between Arabidopsis proteins quantified with MaxQuant and Progenesis QIP was poor due to differential protein inference. Both of these points warrant caution in the interpretation of shotgun proteomics studies. The abundance of around 99% of proteins was constant in repeated sampling of the Arabdiopsis thaliana Col-0 inbred accession; however a handful showed substantial quantitative variability. The function stress/stimulus response was highly significantly overrepresented for these proteins. Heritable information beyond genetic polymorphism that affects gene expression levels has recently been documented for these functions. We speculate on the potential of discovery proteomics to measure gene expression levels as a conduit of the epigenotype shaping quantitative traits.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_04:04:27.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004025
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Wolfgang Hoehenwarter
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-20 23:46:17	ID requested
1	2017-03-07 01:59:43	announced
2	2017-03-09 00:30:27	announced	Updated project metadata.
⏵ 3	2017-10-24 04:04:29	announced	Updated project metadata.

Al Shweiki MR, M, ö, nchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance. J Proteome Res, 16(4):1410-1424(2017) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Shotgun Proteomics, Label-free, Protein Inference, MaxQuant, Progenesis QIP, Scaffold, Arabidopsis, Epigenetics

Wolfgang Hoehenwarter
contact affiliation	Leibniz Institute of Plant Biochemistry
contact email	wolfgang.hoehenwarter@ipb-halle.de
lab head
Wolfgang Hoehenwarter
contact affiliation	Leibniz Institute of Plant Biochemistry
contact email	wolfgang.hoehenwarter@ipb-halle.de
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/2017/03/PXD004025

PRIDE project URI

• PRIDE
  1. PXD004025
     1. Label: PRIDE project
     2. Name: Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance