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ProteomicsThunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highl...
ORGANISM(S): Homo sapiens (Human) 
2024-03-19 | PXD046535 | Pride
Ms2rescore Immunopeptidomics Thunder-dda-pasef Timstof pro 
ProteomicsThunder-DDA-PASEF boosted by MS2rescore enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCoV-2 spike protein epitopes
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highl...
ORGANISM(S): Homo sapiens (Human) 
2024-03-19 | PXD046543 | Pride
Ms2rescore Immunopeptidomics Thunder-dda-pasef Timstof pro 
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
ProteomicsMaximizing immunopeptidomics-based bacterial epitope discovery by rescoring and integrating the results of multiple search engines
Discovery of human leukocyte antigen (HLA) class I presented peptides of bacterial origin is essential to discover bacterial antigen targets as putative vaccine constituents. However, reliable identification of such HLA-presented bacterial epitopes are extremely low abundant compared to the host pro...
ORGANISM(S): Homo sapiens (Human) Listeria monocytogenes EGD 
2025-02-05 | PXD055547 | Pride
ProteomicsThunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with novel MS2PIP timsTOF fragmentation prediction model
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we developed a highl...
ORGANISM(S): Homo Sapiens (human) 
2024-03-18 | PXD040385 | JPOST Repository
UnknownEnhancing peptide identification in metaproteomics through curriculum learning in deep learning.
Not available
S-EPMC12508470 | biostudies-literature
ProteomicsHigher-throughput and sensitive immunopeptidomics profiling
We developed a refined sample preparation workflow that is fully optimized to process low-input and crude samples in 96-well plates, aiming to combine high-throughput with maximal sensitivity. We implemented a miniaturized and automated workflow in a 96-well format using the Tecan Resolvex® A200 liq...
ORGANISM(S): Homo sapiens (Human) 
2026-04-03 | PXD062352 | Pride
Immunopeptidomics Bacterial infection 
ProteomicsEnhancing Peptide Identification in Metaproteomics through Curriculum Learning in Deep Learning
Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from si...
ORGANISM(S): soil metagenome human gut metagenome marine metagenome 
2025-10-20 | PXD067277 | Pride
Lc-ms/ms Marine Human gut Soil 
ProteomicsThe secretome of the white-rot basidiomycete Abortiporus biennis LGAM 436 can cause significant modifications to polystyrene structure
This study focused on investigating the biocatalytic potential of the white-rot basidiomycete Abortiporus biennis LGAM 436 to modify the structure of different types of PS, including amorphous film with atactic stereochemistry and commercial EPS foam. The selection of this specific strain was mainly...
ORGANISM(S): Abortiporus biennis 
2025-04-24 | PXD058977 | Pride
Polystyrene Lfq Plastic pollution Biodegradation Abortiporus Fungi White-rot Secretome Quantms Dda 
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