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View article: MHCquant2 refines immunopeptidomics tumor antigen discovery
MHCquant2 refines immunopeptidomics tumor antigen discovery Open
Confident identification of human leukocyte antigen (HLA)-presented peptides is crucial for advancing cancer immunotherapy. We present MHCquant2, a scalable and modular Nextflow pipeline integrated into nf-core as a reproducible, portable,…
View article: Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep
Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep Open
Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysis of proteomics data, for example for i…
View article: DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups
DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups Open
While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These variations can render retention time predict…
View article: Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring
Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring Open
Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is cha…
View article: Collisional cross-section prediction for multiconformational peptide ions with IM2Deep
Collisional cross-section prediction for multiconformational peptide ions with IM2Deep Open
Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysis of proteomics data, for example for i…
View article: Boosting metaproteomics identification rates and taxonomic specificity with MS<sup>2</sup>Rescore
Boosting metaproteomics identification rates and taxonomic specificity with MS<sup>2</sup>Rescore Open
Background Metaproteomics, the study of the collective proteome within microbial ecosystems, has gained increasing interest over the past decade. However, peptide identification rates in metaproteomics remain low compared to single-species…
View article: TIMS<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
TIMS<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 Open
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…
View article: MHCquant2 refines immunopeptidomics tumor antigen discovery
MHCquant2 refines immunopeptidomics tumor antigen discovery Open
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 …
View article: Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring
Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring Open
Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is cha…
View article: High-coverage immunopeptidomics using timsTOF mass spectrometers with Thunder-DDA-PASEF boosted by MS2Rescore
High-coverage immunopeptidomics using timsTOF mass spectrometers with Thunder-DDA-PASEF boosted by MS2Rescore Open
Major histocompatibility complex (MHC, or Human leukocyte antigen, HLA) peptide ligands can be exploited to develop immunotherapies targeting immunogenic disease-specific immunopeptides, such as virus- or cancer mutation-derived peptides. …
View article: TIMS<sup>2</sup>Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS<sup>2</sup>Rescore
TIMS<sup>2</sup>Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS<sup>2</sup>Rescore Open
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…
View article: Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links
Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links Open
In protein‐RNA cross‐linking mass spectrometry, UV or chemical cross‐linking introduces stable bonds between amino acids and nucleic acids in protein‐RNA complexes that are then analyzed and detected in mass spectra. This analytical tool d…
View article: MS<sup>2</sup>Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0
MS<sup>2</sup>Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 Open
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We introd…
View article: Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model Open
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 abu…
View article: MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0
MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0 Open
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We here i…
View article: MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0
MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0 Open
Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We here i…
View article: Data for "MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0"
Data for "MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0" Open
This data set contains reanalyzed data from the "MS2 500 ms" and "MS2 750 ms" workflow originally published by Furtwängler et al. 2022. The full data set is available on ProteomeXchange via the PRIDE partner repository using ID PXD029320. …
View article: Data for "MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0"
Data for "MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0" Open
This data set contains reanalyzed data from the "MS2 500 ms" and "MS2 750 ms" workflow originally published by Furtwängler et al. 2022. The full data set is available on ProteomeXchange via the PRIDE partner repository using ID PXD029320. …
View article: Ionmob: a Python package for prediction of peptide collisional cross-section values
Ionmob: a Python package for prediction of peptide collisional cross-section values Open
Motivation Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived mobility of an ion to its collisional cro…
View article: Updated MS²PIP web server supports cutting-edge proteomics applications
Updated MS²PIP web server supports cutting-edge proteomics applications Open
Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such as immunopeptidomi…
View article: Data sets for "Updated MS²PIP web server supports cutting-edge proteomics applications"
Data sets for "Updated MS²PIP web server supports cutting-edge proteomics applications" Open
Data sets and code used to train and evaluate new MS²PIP models.
View article: Data sets for "Extended MS²PIP web server enables new proteomics applications"
Data sets for "Extended MS²PIP web server enables new proteomics applications" Open
Data sets used to train and evaluate new MS²PIP models.
View article: Data sets for "Updated MS²PIP web server supports cutting-edge proteomics applications"
Data sets for "Updated MS²PIP web server supports cutting-edge proteomics applications" Open
Data sets and code used to train and evaluate new MS²PIP models.
View article: Ionmob: A Python Package for Prediction of Peptide Collisional Cross-Section Values
Ionmob: A Python Package for Prediction of Peptide Collisional Cross-Section Values Open
Pre-processed datasets used to train machine learning models of ionmob python package: https://github.com/theGreatHerrLebert/ionmob
View article: Ionmob: A Python Package for Prediction of Peptide Collisional Cross-Section Values
Ionmob: A Python Package for Prediction of Peptide Collisional Cross-Section Values Open
Pre-processed datasets used to train machine learning models of ionmob python package: https://github.com/theGreatHerrLebert/ionmob
View article: psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results
psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results Open
A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist…
View article: Supporting data for "Quality control for the target decoy approach for peptide identification"
Supporting data for "Quality control for the target decoy approach for peptide identification" Open
Supporting data for the manuscript "Quality control for the target decoy approach for peptide identification". Input files are raw mass spectrometry runs, to be downloaded from the PRIDE Archive (https://www.ebi.ac.uk/pride/), which can be…
View article: Supporting data for "Quality control for the target decoy approach for peptide identification"
Supporting data for "Quality control for the target decoy approach for peptide identification" Open
Supporting data for the manuscript "Quality control for the target decoy approach for peptide identification". Input files are raw mass spectrometry runs, to be downloaded from the PRIDE Archive (https://www.ebi.ac.uk/pride/), which can be…
View article: psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results
psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results Open
A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist…