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ProteomicsEvaluation of different data-driven rescoring platforms to increase peptide identifications in HeLa digest samples
Evaluate the performance of different rescoring platforms with the aim of standardizing pipelines within our research group.
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD052875 | Pride
Hela samples Rescoring pipelines 
ProteomicsMS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Immunopeptidomics aims to identify Major Histocompatibility Complex-presented peptides on every cell that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the non-tryptic nature of immunopeptides, complicating their identificatio...
ORGANISM(S): Homo sapiens (Human) 
2022-07-11 | PXD033868 | Pride
Q exactive hf-x Human Immunopeptidomics 
UnknownMS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.
Not available
S-EPMC9411678 | biostudies-literature
UnknownComparative Analysis of Data-Driven Rescoring Platforms for Improved Peptide Identification in HeLa Digest Samples.
Not available
S-EPMC11962579 | biostudies-literature
ProteomicsIntegrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage
We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this ability to generate large datasets through multienzyme deep proteomics experiments for characterisa...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Escherichia coli 
2026-03-13 | PXD065289 | Pride
Ecd Eid Uvpd 
UnknownEnhancing Mass spectrometry-based tumor immunopeptide identification: machine learning filter leveraging HLA binding affinity, aliphatic index and retention time deviation.
Not available
S-EPMC10864759 | biostudies-literature
UnknownIntegrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage.
Not available
S-EPMC12154582 | biostudies-literature
UnknownPgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.
Not available
S-EPMC10825656 | biostudies-literature
ProteomicsPCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development
Various cancer immunotherapies rely on the T cell recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remain...
ORGANISM(S): Homo sapiens (Human) 
2025-04-04 | PXD058376 | Pride
Human Lc-msms Synthetic peptides 
ProteomicsMHCquant2 refines immunopeptidomics tumor antigen discovery
The identification of human leukocyte antigen (HLA)-presented peptides as targets of anti-cancer T cell response is pivotal for the development of novel immunotherapies. Mass spectrometry (MS)-based immunopeptidomics enables the detection of these peptides, yet confident identifications and thus imp...
ORGANISM(S): Homo sapiens (Human) 
2025-08-22 | PXD058436 | Pride
Immunopeptidomics Nf-core Mhcquant Pipeline Dda 
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