PXD069521-1

PXD069521 is an original dataset announced via ProteomeXchange.

Title	Generation of peptide detectability datasets]{Generation of peptide detectability datasets from single DIA spectra for prediction model fine-tuning
Description	Knowing which peptide can be detected during a mass spectrometry based proteomics analysis is a valuable information. Detectability prediction models predict detectability based on peptides amino acid sequences. Since peptide detectability varies substantially across different instruments, acquisition methods, and experimental conditions, sequence-based models alone cannot account for these sources of variability. Recent state-of-the-art methods address this transferability limitation by fine tuning specific models for each experimental setup. Nonetheless, these methods rely on significantly large training detectability datasets attaining 300k peptides, which incurs substantial costs both in terms of acquisition and processing times. In this study we propose a complementary method to infer detectability dataset from a single DIA spectrum. Such datasets can then be used to fine-tune prediction models from limited raw data while improving transferability to any specific setup. The associated goal is to further promote the use of detectability models in proteomics pipelines by cutting the underlying costs. For instance, we show that filtering search library based on predicted detectability simultaneously improve peptide identification and reduce computing time.
HostingRepository	PRIDE
AnnounceDate	2025-10-27
AnnouncementXML	Submission_2025-10-27_03:33:38.667.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leo Schneider
SpeciesList	scientific name: Faecalibacterium prausnitzii; NCBI TaxID: NEWT:853; scientific name: Staphylococcus epidermidis; NCBI TaxID: NEWT:1282; scientific name: Lacticaseibacillus casei; NCBI TaxID: NEWT:1582; scientific name: Veillonella rogosae; NCBI TaxID: NEWT:423477; scientific name: Clostridium perfringens; NCBI TaxID: NEWT:1502; scientific name: Candida albicans (Yeast); NCBI TaxID: NEWT:5476; scientific name: Streptococcus agalactiae STIR-CD-17; NCBI TaxID: NEWT:1097670; scientific name: Enterococcus faecalis (Streptococcus faecalis); NCBI TaxID: NEWT:1351; scientific name: Salmonella enterica subsp. enterica serovar Rissen str. 150; NCBI TaxID: NEWT:687914; scientific name: Fusobacterium nucleatum; NCBI TaxID: NEWT:851; scientific name: Enterobacter cloacae; NCBI TaxID: NEWT:550; scientific name: Bifidobacterium adolescentis; NCBI TaxID: NEWT:1680; scientific name: Akkermansia muciniphila; NCBI TaxID: NEWT:239935; scientific name: Haemophilus influenzae; NCBI TaxID: NEWT:727; scientific name: Roseburia hominis; NCBI TaxID: NEWT:301301; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Bacteroides fragilis; NCBI TaxID: NEWT:817; scientific name: Methanobrevibacter smithii; NCBI TaxID: NEWT:2173; scientific name: Prevotella corporis; NCBI TaxID: NEWT:28128; scientific name: Klebsiella pneumoniae; NCBI TaxID: NEWT:573; scientific name: Clostridioides difficile; NCBI TaxID: NEWT:1496; scientific name: Limosilactobacillus fermentum; NCBI TaxID: NEWT:1613; scientific name: Aerococcus viridans; NCBI TaxID: NEWT:1377;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral; ZenoTOF 7600+

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-16 04:09:11	ID requested
⏵ 1	2025-10-27 03:33:39	announced

Dataset with its publication pending

submitter keyword: DIA, detectability

Emmanuelle Vulliet
contact affiliation	director
contact email	emmanuelle.vulliet@isa-lyon.fr
lab head
Leo Schneider
contact affiliation	Université Lyon 1
contact email	schneider.leo@free.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/2025/10/PXD069521

PRIDE project URI

• PRIDE
  1. PXD069521
     1. Label: PRIDE project
     2. Name: Generation of peptide detectability datasets]{Generation of peptide detectability datasets from single DIA spectra for prediction model fine-tuning