PXD012782-3

PXD012782 is an original dataset announced via ProteomeXchange.

Title	PNGase-F treated and untreated peptides from primary human mesenchymal stem cells for protein/PTM quant benchmarking
Description	Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behaviour of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment, and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:54:02.561.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Venkatesh Mallikarjun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	(18)O label at both C-terminal oxygens; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-19 05:19:07	ID requested
1	2019-03-11 17:31:51	announced
2	2020-04-26 22:58:32	announced	2020-04-27: Updated publication reference for PubMed record(s): 32319298.
⏵ 3	2024-10-22 04:54:05	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.9b00468;

Mallikarjun V, Richardson SM, Swift J, BayesENproteomics: Bayesian Elastic Nets for Quantification of Peptidoforms in Complex Samples. J Proteome Res, 19(6):2167-2184(2020) [pubmed]

curator keyword: Technical

submitter keyword: BayesENProteomics, PNGase-F, mesenchymal stem cell

Joe Swift
contact affiliation	Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester
contact email	joe.swift@manchester.ac.uk
lab head
Venkatesh Mallikarjun
contact affiliation	University of Manchester
contact email	venkatesh.mallikarjun@manchester.ac.uk
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/2019/03/PXD012782

PRIDE project URI

• PRIDE
  1. PXD012782
     1. Label: PRIDE project
     2. Name: PNGase-F treated and untreated peptides from primary human mesenchymal stem cells for protein/PTM quant benchmarking