PXD007683

PXD007683 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide evaluation of two common protein quantification methods
Description	Proteomics experiments commonly aim to estimate and detect differential abundance across all expressed proteins. Within this experimental design, some of the most challenging measurements are small fold changes for lower abundance proteins. While bottom-up proteomics methods are approaching comprehensive coverage of even complex eukaryotic proteomes, failing to reliably quantify lower abundance proteins can limit the precision and reach of experiments to much less than the identified -let alone total- proteome. Here we test the ability of two common methods, a tandem mass tagging (TMT) method and a label- free quantitation method (LFQ), to achieve comprehensive quantitative coverage by benchmarking their capacity to measure 3 different levels of change (3-, 2-, and 1.5-fold) across an entire dataset. Both methods achieved comparably accurate estimates for all three fold-changes. However, the TMT method detected changes that reached statistical significance three times more often due to higher precision and fewer missing values. These findings highlight the importance of refining proteome quantitation methods to bring the number of usefully quantified proteins into closer agreement with the number of total quantified proteins.
HostingRepository	PRIDE
AnnounceDate	2018-04-05
AnnouncementXML	Submission_2019-03-07_05:46:11.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-07 02:07:36	ID requested
1	2018-04-05 03:08:02	announced
⏵ 2	2019-03-07 05:46:12	announced	Updated publication reference for PubMed record(s): 29635916.

O'Connell JD, Paulo JA, O'Brien JJ, Gygi SP, Proteome-Wide Evaluation of Two Common Protein Quantification Methods. J Proteome Res, 17(5):1934-1942(2018) [pubmed]

curator keyword: Technical

submitter keyword: LFQ, TMT, MaxQuant

Steven P. Gygi
contact affiliation	Cell Biology, Harvard Medical School, Boston, MA, USA
contact email	sgygi@hms.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
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/2018/04/PXD007683

PRIDE project URI

• PRIDE
  1. PXD007683
     1. Label: PRIDE project
     2. Name: Proteome-wide evaluation of two common protein quantification methods