PXD035198

PXD035198 is an original dataset announced via ProteomeXchange.

Title	Stability assessment of the human proteotypic peptides for proteomics quantification
Description	Mass spectrometry coupled to liquid chromatography is one of the most powerful technologies for proteome quantification in a variety of biomedical samples, including cells, tissues and liquid biopsies. In peptide-centric workflows protein mixtures proteins are enzymatically digested to peptides prior their analysis. Experimental spectra are used for peptide identification, and extracted peptide areas, peak heights, or spectral counts are used to infer protein quantities using different heuristics. However, proteome-wide quantification studies rarely identify all potential peptides for any given protein while targeted proteomics experiments focus on a set of peptides for the proteins of interest. Consequently, proteomics methods rely on the use of a limited subset of all possible peptides as proxies for protein quantitation, which are specified either prior or after data acquisition. Several studies have evaluated the quantitative response of tryptic peptides and have described rules to guide peptide selection for protein quantification. However, beyond the effect of tryptic digestion and missed cleavages, short and mid-term peptide stability can also have a profound effect on the measurement reproducibility, specially when analysing proteomics samples from large cohorts of patients that expand for several days or weeks of measurement. In this project we assessed the stability of more than 100,000 peptides from the proteotypic peptide set of the Proteome Tools collection, and we used the obtained experimental data to train and validate a new peptide stability predictor for proteomics quantification.
HostingRepository	PRIDE
AnnounceDate	2025-02-24
AnnouncementXML	Submission_2025-02-24_06:55:32.128.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-09 08:53:22	ID requested
⏵ 1	2025-02-24 06:55:32	announced

10.1021/ACS.ANALCHEM.3C02269;

submitter keyword: proteotypic, Proteome Tools,peptide stability, quantitation

Eduard Sabidó
contact affiliation	Head of the CRG/UPF Proteomics Unit Centre for Genomic Regulation (CRG)
contact email	eduard.sabido@crg.cat
lab head
Cristina Chiva
contact affiliation	University Pompeu Fabra
contact email	cristina.chiva@upf.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/2025/02/PXD035198

PRIDE project URI

• PRIDE
  1. PXD035198
     1. Label: PRIDE project
     2. Name: Stability assessment of the human proteotypic peptides for proteomics quantification