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ProteomicsDDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics
This project provides a large-scale training dataset for DDA-BERT, an end-to-end transformer-based deep learning model developed for PSM rescoring in data-dependent acquisition (DDA) proteomics. The dataset comprises curated PSMs generated using established database search engines, including FragPip...
ORGANISM(S): Chlamydomonas reinhardtii Glycine max Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans Rattus norvegicus (Rat) Bacillus cereus Bacillus subtilis 
2026-08-24 | PXD072999 | Pride
Deep learning Dda proteomics Peptide-spectrum matches (psms) rescoring Dda-bert Peptide identification 
ProteomicsRescoring approaches improve consensus in peptide identification across diverse search engines and datasets - CAMPI reanalysis
Peptide–spectrum match (PSM) rescoring has become standard in proteomics workflows, improving peptide identification accuracy across diverse search engines. Despite the availability of multiple rescoring strategies, systematic comparisons spanning several search engines, datasets, and database confi...
ORGANISM(S): Lactobacillus plantarum Anaerostipes caccae Thomasclavelia ramosa Bacteroides thetaiotaomicron Escherichia coli Bifidobacterium longum Blautia producta Clostridium butyricum 
2026-09-11 | PXD075141 | Pride
Rescoring Reanalysis Metaproteomics Comparison Proteomics 
ProteomicsRescoring approaches improve consensus in peptide identification across diverse search engines and datasets - timsTOF benchmark reanalysis
Peptide–spectrum match (PSM) rescoring has become standard in proteomics workflows, improving peptide identification accuracy across diverse search engines. Despite the availability of multiple rescoring strategies, systematic comparisons spanning several search engines, datasets, and database confi...
ORGANISM(S): Homo sapiens (Human) 
2026-09-11 | PXD075206 | Pride
Rescoring Reanalysis Metaproteomics Comparison Proteomics 
ProteomicsRescoring approaches improve consensus in peptide identification across diverse search engines and datasets - Orbitrap benchmark reanalysis
Peptide–spectrum match (PSM) rescoring has become standard in proteomics workflows, improving peptide identification accuracy across diverse search engines. Despite the availability of multiple rescoring strategies, systematic comparisons spanning several search engines, datasets, and database confi...
ORGANISM(S): Homo sapiens (Human) 
2026-09-11 | PXD075209 | Pride
Rescoring Reanalysis Metaproteomics Comparison Proteomics 
ProteomicsRescoring approaches improve consensus in peptide identification across diverse search engines and datasets - Cancer Array reanalysis
Peptide–spectrum match (PSM) rescoring has become standard in proteomics workflows, improving peptide identification accuracy across diverse search engines. Despite the availability of multiple rescoring strategies, systematic comparisons spanning several search engines, datasets, and database confi...
ORGANISM(S): Homo sapiens (Human) 
2026-09-11 | PXD075199 | Pride
Rescoring Reanalysis Metaproteomics Comparison Proteomics 
UnknownProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer.
Not available
S-EPMC11976853 | biostudies-literature
ProteomicsData-driven rescoring meets identification transfer in multi-batch isobaric labeling experiments: the best of both worlds (ProSIMSIt)
Multi-batch isobaric labeling experiments are frequently applied for clinical and pharmaceutical studies of large sample cohorts. To tackle the critical issue of missing values in such studies, we introduce the ProSIMSIt pipeline. It combines the advantages of tandem mass spectrum clustering via SIM...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD057211 | Pride
Prediction Missing values Isobaric labelling Simsi-transfer Oktoberfest Maxquant 
UnknownPgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.
Not available
S-EPMC10825656 | biostudies-literature
ProteomicsBCMA ubiquitylation in multiple myeloma
Mass spectrometric analysis of MM cell-purified B-cell maturation antigen (BCMA) protein to identify ubiquitylation sites.
ORGANISM(S): Homo sapiens (Human) 
2025-07-29 | PXD056372 | Pride
Ubiquitylation Bcma Di-glycine Ubiquitin 
ProteomicsProteomic profiling of WT and KO for DPP3 Mus musculus splenocites, treated (and not) with LPS
Effective host defense against infection relies on the tight coordination of immune activation, metabolic adaptation, and redox control, yet how these processes are integrated remains incompletely understood. Here, we identify dipeptidyl peptidase 3 (Dpp3) as a negative regulator of antimicrobial im...
ORGANISM(S): Mus musculus (Mouse) 
2026-05-21 | PXD074007 | Pride
Mus musculus Immunity Splenocites 
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