PXD043476

PXD043476 is an original dataset announced via ProteomeXchange.

Title	msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Description	In the era of open-modification search engines, more post-translational modifications than ever can be detected by LC-MS/MS-based proteomics. This development can switch proteomics research into a higher gear, as PTMs are key in many cellular pathways important in cell proliferation, migration, metastasis and ageing. However, despite these advances in modification identification, statistical methods for PTM-level quantification and differential analysis have yet to catch up. This absence can partly be explained by the inherently low abundance of many PTMs and the confounding of PTM intensities with its parent protein abundance. Therefore, we have developed msqrob2PTM, a new workflow in the msqrob2 universe capable of differential abundance analysis at the PTM, and at the peptidoform level. The latter is important for validating significantly found PTMs. Indeed, as our method can deal with multiple PTMs per peptidoform, there is a possibility that significant PTMs stem from one significant peptidoform carrying another PTM, hinting that it might the other PTM driving the perceived differential abundance. Our workflows can flag both Differential Peptidoform (PTM) Abundance (DPA) and Differential Peptidoform (PTM) Usage (DPU). This enables a distinction between direct assessment of differential abundance of peptidoforms (DPA), and differences in the relative usage of peptidoforms corrected for corresponding protein abundances (DPU). For DPA, we directly model the log2-transformed peptidoform (PTM) intensities, while for DPU, we correct for parent protein abundance by an intermediate normalisation step which calculates the log2-ratio of the peptidoform (PTM) intensities to their summarized parent protein intensities. We demonstrated the utility and performance of msqrob2PTM by applying it on datasets with known ground truth, as well as on biological PTM-rich datasets. Our results show that msqrob2PTM is on par with, or surpassing the performance of, the current state-of-the-art method, MSstatsPTM. Moreover, msqrob2PTM is currently unique in providing output at the peptidoform level.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:45:58.940.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marie GEBELIN
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-03 02:40:52	ID requested
1	2024-06-16 03:49:24	announced
⏵ 2	2024-10-22 06:46:01	announced	2024-10-22: Updated project metadata.

Demeulemeester N, G, é, belin M, Caldi Gomes L, Lingor P, Carapito C, Martens L, Clement L, msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level. Mol Cell Proteomics, 23(2):100708(2024) [pubmed]

10.1016/j.mcpro.2023.100708;

submitter keyword: msqrob2PTM, PTM, msqrob, peptidoform

Christine Carapito
contact affiliation	Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg
contact email	ccarapito@unistra.fr
lab head
Marie GEBELIN
contact affiliation	Laboratoire de Spectometrie de Mass Bio-Organique, IPHC, CNRS
contact email	marie.gebelin@etu.unistra.fr
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/2024/06/PXD043476

PRIDE project URI

• PRIDE
  1. PXD043476
     1. Label: PRIDE project
     2. Name: msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level