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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 
ProteomicsTIMS²Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS²Rescore - Plasma proteomics
The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields – such as plasma pro...
ORGANISM(S): Homo sapiens (Human) 
2025-02-17 | PXD053748 | Pride
Plasma Data-driven rescoring 
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 
UnknownProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer.
Not available
S-EPMC11976853 | biostudies-literature
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
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 
UnknownTIMS<sup>2</sup>Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS<sup>2</sup>Rescore.
Not available
S-EPMC11894666 | biostudies-literature
ProteomicsProsit-XL: enhanced cross-linked peptide identification by accurate fragment intensity prediction to study protein-protein interactions and protein structures
It has been shown that integrating peptide property predictions such as fragment intensity into the scoring process of peptide spectrum match can greatly increase the number of confidently identified peptides compared to using traditional scoring methods. Here, we introduce Prosit-XL, a robust and a...
ORGANISM(S): Homo sapiens (Human) Cytomegalovirus 
2025-05-18 | PXD057705 | Pride
Deep learning Crosslinking mass spectrometry 
ProteomicsPSMB4 pulldown ID with PSMD5 overexpression
For PSMD5 over expression experiment, PSMB4-tagged cells were transfected in either 6-well plates (Cat. No. 3506; Costar) or 10 cm dishes using 1 µg or 5 µg of HA-PSMD5 or HA-PSMD5ΔCT, respectively. All the transfections were performed with Lipofectamine 3000 (Cat. No. L3000015; Thermo Fisher Scient...
ORGANISM(S): Homo sapiens (Human) 
2026-07-16 | PXD076795 | Pride
Psmd5 Proteasome 
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