PXD001426-1

PXD001426 is an original dataset announced via ProteomeXchange.

Title	EBprot: Bayesian Analysis of Labelling-based Quantitative Proteomics Data
Description	Labelling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs) between biological samples. The current data analysis platform relies on protein-level ratios, where peptide-level ratios are averaged to yield a single summary ratio for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is incorporated into the differential expression (DE) analysis. Here we propose a novel probabilistic framework EBprot that directly models the peptide-to-protein hierarchy and rewards the proteins with reproducible quantification over multiple peptides. To evaluate its performance with known DE states, we first verified that the peptide-level analysis of EBprot provides more accurate estimation of the false discovery rates and better receiver-operating characteristic than other protein ratio analyses using simulation datasets, and confirmed the superior classification performance in a UPS1 mixture spike-in dataset. To illustrate the performance of EBprot in realistic applications, we applied EBprot to a SILAC dataset for lung cancer subtype analysis and an iTRAQ dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells, each featuring a different experimental design. Through these various examples, we show that the peptide-level analysis of EBprot provides a competitive advantage over alternative methods for the DE analysis of labelling-based quantitative datasets.
HostingRepository	PRIDE
AnnounceDate	2015-06-29
AnnouncementXML	Submission_2015-06-29_10:10:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rachel Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-10-21 02:23:25	ID requested
⏵ 1	2015-06-29 10:10:11	announced
2	2024-10-22 04:02:59	announced	2024-10-22: Updated project metadata.

Koh HW, Swa HL, Fermin D, Ler SG, Gunaratne J, Choi H, EBprot: Statistical analysis of labeling-based quantitative proteomics data. Proteomics, 15(15):2580-91(2015) [pubmed]

curator keyword: Technical

submitter keyword: Stable isotope labelling, Quantitative analysis, Differential expression, Hierarchical mixture model

Hyung Won Choi
contact affiliation	NUS
contact email	hyung_won_choi@nuhs.edu.sg
lab head
Rachel Li
contact affiliation	IMCB
contact email	hxli@imcb.a-star.edu.sg
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/2015/06/PXD001426

PRIDE project URI

• PRIDE
  1. PXD001426
     1. Label: PRIDE project
     2. Name: EBprot: Bayesian Analysis of Labelling-based Quantitative Proteomics Data