PXD054189

PXD054189 is an original dataset announced via ProteomeXchange.

Title	Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics
Description	Mass spectrometry-based proteomics has advanced with the integration of experimental and predicted spectral libraries, which have significantly improved peptide identification in complex search spaces. However, challenges persist in distinguishing some peptides with close retention times and nearly identical fragmentation patterns. In this study, we conducted a theoretical assessment to quantify the prevalence of indistinguishable peptides within the human canonical proteome and immunopeptidome using state-of-the-art retention time and spectrum prediction models. By quantifying the proportion of peptides posing challenges to unequivocal identification, we set the accessible portion within a given proteome, thus establishing the current boundaries of the field, and underscore the effectiveness of contemporary analytical methodologies in resolving the complexity of the human proteome and immunopeptidome via mass spectrometry.
HostingRepository	PRIDE
AnnounceDate	2024-10-11
AnnouncementXML	Submission_2024-10-11_01:00:48.120.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eduard Sabidó
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-24 11:23:38	ID requested
⏵ 1	2024-10-11 01:00:58	announced

10.1021/acs.analchem.4c02803;

Elhamraoui Z, Borr, à, s E, Wilhelm M, Sabid, ó E, Theoretical Assessment of Indistinguishable Peptides in Mass Spectrometry-Based Proteomics. Anal Chem, 96(40):15829-15833(2024) [pubmed]

submitter keyword: Hela, proteomics, DIA

Eduard Sabidó
contact affiliation	Centre for Genomic Regulation, Universitat Pompeu Fabra
contact email	eduard.sabido@crg.cat
lab head
Eduard Sabidó
contact affiliation	Centre de Regulació Genòmica
contact email	eduard.sabido@crg.cat
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/2024/10/PXD054189

PRIDE project URI

• PRIDE
  1. PXD054189
     1. Label: PRIDE project
     2. Name: Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics