PXD063099 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | DEqMS - a method for differential protein expression analysis of quantitative mass spectrometry data |
| Description | DEqMS is a statistical method to perform differential protein expression (abundance) analysis for quantitative mass spectrometry-based proteomics. Developed on top of Limma, DEqMS implements a robust Bayesian method for accurate variance estimation while taking into account the number of peptide precursors or PSMs used for protein quantification. DEqMS has a demonstrated improved accuracy and statistical power compared to previous methods and has since its initial publication been used by a wide range of researchers in various proteomics applications. Originally, DEqMS was validated to analyze proteomics data from data dependent acquisition (DDA). Based on users’ feedback, we now demonstrate DEqMS usability in performing differential analysis also in data independent acquisition (DIA)-based proteomics data. Given this updated protocol, we envision that DEqMS will continue to be a useful tool for defining sets of proteins with significantly different levels between sample groups based on complex quantitative proteomics data. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-06-03 |
| AnnouncementXML | Submission_2026-06-03_10:37:54.845.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Georgios Mermelekas |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | iodoacetamide derivatized residue |
| Instrument | Bruker Daltonics timsTOF series; Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-04-18 03:37:51 | ID requested | |
| ⏵ 1 | 2026-06-03 10:37:55 | announced | |
Publication List
| Zhu Y, Berkovska O, Wang L, Yang M, Johansson HJ, Mermelekas G, Zarrineh M, Yin D, Orre LM, Lehti, ö J, Differential protein expression analysis of quantitative mass spectrometry data using DEqMS. Nat Protoc, ():(2026) [pubmed] |
| 10.1038/s41596-026-01349-7; |
Keyword List
| submitter keyword: differential abundance, DIA, label-free proteomics, statistical method,Differential expression, LC-MS/MS |
Contact List
| Janne Lehtiö |
|---|
| contact affiliation | Department of oncology and pathology, Karolinska Institute, Stockholm, Sweden |
| contact email | janne.lehtio@ki.se |
| lab head | |
| Georgios Mermelekas |
|---|
| contact affiliation | Karolinska Institutet |
| contact email | georgios.mermelekas@scilifelab.se |
| dataset submitter | |
Full Dataset Link List
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/2026/06/PXD063099 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD063099
- Label: PRIDE project
- Name: DEqMS - a method for differential protein expression analysis of quantitative mass spectrometry data
