Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Arthur Declercq
iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications Click to copy article link Article link copied!
Introduction Click to copy section linkSection link copied! In liquid chromatography–mass spectrometry (LC-MS) proteomics, retention time refers to the specific duration it takes for a peptide to traverse the chromatography column and reach the MS detector. Chromatographic separation and its associated retention time value serve as an additional dimension that separates peptides prior to analysis and thus substantially reduce sample complexity in the acquired MS dimensions.
Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups - Nature Communications
Abstract 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 prediction models inaccurate and dramatically reduce the value of predictions for identification, validation, and DIA spectral library generation.
Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep
Introduction Click to copy section linkSection link copied! Recent advances in LC–IM–MS/MS technology have strongly enhanced identification capabilities in complex proteomics workflows. (1−3) Traditionally, LC–MS/MS systems solely depended on liquid chromatography and mass analyzers for peptide separation and selection before fragmentation.
Collisional cross-section prediction for multiconformational peptide ions with IM2Deep
Abstract 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 identification or quantification through feature finding. Here, we present an improved version of IM2Deep that is trained on a carefully curated dataset to predict CCS values of multiconformational peptides.
Boosting metaproteomics identification rates and taxonomic specificity with MS2Rescore
Abstract 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 proteomics. A key challenge is the limited sequence resolution of current identification algorithms, which were primarily designed for single-species analyses.
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore
Introduction Click to copy section linkSection link copied! Proteomics is an invaluable tool for understanding human biology, facilitating the discovery of new disease biomarkers, identifying potential therapeutic targets, and exploring interactions with pathogens or microorganisms. (1−4) Various proteomics subfields have emerged that address specific challenges.
TIMS2Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS2Rescore
Introduction Click to copy section linkSection link copied! Proteomics is an invaluable tool for understanding human biology, facilitating the discovery of new disease biomarkers, identifying potential therapeutic targets, and exploring interactions with pathogens or microorganisms. (1−4) Various proteomics subfields have emerged that address specific challenges.
TIMS2Rescore: A DDA-PASEF optimized data-driven rescoring pipeline based on MS2Rescore
Abstract 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 proteomics, immunopeptidomics, and metaproteomics - must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments.
Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links
LC-MS liquid chromatography mass spectrometry PARs photoactivatable ribonucleosides UV ultraviolet 4SU 4-thiouridine NM nitrogen mustard DEB diepoxybutane RBPs RNA binding proteins TiO2 titanium dioxide PTMs post-translational modifications MS/MS tandem mass spectra HCD high-energy collision-induced dissociation FDR false discovery rate PSMs peptide-spectrum matches CSMs crosslink-spectrum matches FMR false match rate 1 INTRODUCTION Interactions between proteins and RNA are important for many...
MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Proteome Res. 2024, XXXX, XXX Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).
MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Arthur
Contact Arthur, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack