Search Results - "Bouwmeester, Robbin"

DeepLC can predict retention times for peptides that carry as-yet unseen modifications by Bouwmeester, Robbin, Gabriels, Ralf, Hulstaert, Niels, Martens, Lennart, Degroeve, Sven

“…The inclusion of peptide retention time prediction promises to remove peptide identification ambiguity in complex liquid chromatography–mass spectrometry…”
Get full text

Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit by Boone, Morgane, Ramasamy, Pathmanaban, Zuallaert, Jasper, Bouwmeester, Robbin, Van Moer, Berre, Maddelein, Davy, Turan, Demet, Hulstaert, Niels, Eeckhaut, Hannah, Vandermarliere, Elien, Martens, Lennart, Degroeve, Sven, De Neve, Wesley, Vranken, Wim, Callewaert, Nico

Get full text

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit by Boone, Morgane, Ramasamy, Pathmanaban, Zuallaert, Jasper, Bouwmeester, Robbin, Van Moer, Berre, Maddelein, Davy, Turan, Demet, Hulstaert, Niels, Eeckhaut, Hannah, Vandermarliere, Elien, Martens, Lennart, Degroeve, Sven, De Neve, Wesley, Vranken, Wim, Callewaert, Nico

“…While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to…”
Get full text

Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection by Salz, Renee, Bouwmeester, Robbin, Gabriels, Ralf, Degroeve, Sven, Martens, Lennart, Volders, Pieter-Jan, ’t Hoen, Peter A.C

“…Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized proteomics. Both the…”
Get full text

The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions by Sakarika, Myrsini, Kerckhof, Frederiek-Maarten, Van Peteghem, Lotte, Pereira, Alexandra, Van Den Bossche, Tim, Bouwmeester, Robbin, Gabriels, Ralf, Van Haver, Delphi, Ulčar, Barbara, Martens, Lennart, Impens, Francis, Boon, Nico, Ganigué, Ramon, Rabaey, Korneel

“…It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in…”
Get full text

Comprehensive and Empirical Evaluation of Machine Learning Algorithms for Small Molecule LC Retention Time Prediction by Bouwmeester, Robbin, Martens, Lennart, Degroeve, Sven

“…Liquid chromatography is a core component of almost all mass spectrometric analyses of (bio)­molecules. Because of the high-throughput nature of mass…”
Get full text

Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times by Bouwmeester, Robbin, Martens, Lennart, Degroeve, Sven

“…Accurate prediction of liquid chromatographic retention times from small-molecule structures is useful for reducing experimental measurements and for improved…”
Get full text

MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates by Declercq, Arthur, Bouwmeester, Robbin, Hirschler, Aurélie, Carapito, Christine, Degroeve, Sven, Martens, Lennart, Gabriels, Ralf

“…Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in anti-cancer vaccine…”
Get full text

Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins by Claeys, Tine, Menu, Maxime, Bouwmeester, Robbin, Gevaert, Kris, Martens, Lennart

“…Using data from 183 public human data sets from PRIDE, a machine learning model was trained to identify tissue and cell-type specific protein patterns. PRIDE…”
Get full text

psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results by Gabriels, Ralf, Declercq, Arthur, Bouwmeester, Robbin, Degroeve, Sven, Martens, Lennart

“…A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream…”
Get full text

The Age of Data‐Driven Proteomics: How Machine Learning Enables Novel Workflows by Bouwmeester, Robbin, Gabriels, Ralf, Van Den Bossche, Tim, Martens, Lennart, Degroeve, Sven

“…A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics,…”
Get full text

Graph Convolutional Networks for Improved Prediction and Interpretability of Chromatographic Retention Data by Kensert, Alexander, Bouwmeester, Robbin, Efthymiadis, Kyriakos, Van Broeck, Peter, Desmet, Gert, Cabooter, Deirdre

“…Machine learning is a popular technique to predict the retention times of molecules based on descriptors. Descriptors and associated labels (e.g., retention…”
Get full text

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions by C Silva, Ana S, Bouwmeester, Robbin, Martens, Lennart, Degroeve, Sven

“…The use of post-processing tools to maximize the information gained from a proteomics search engine is widely accepted and used by the community, with the most…”
Get full text

Updated MS²PIP web server supports cutting-edge proteomics applications by Declercq, Arthur, Bouwmeester, Robbin, Chiva, Cristina, Sabidó, Eduard, Hirschler, Aurélie, Carapito, Christine, Martens, Lennart, Degroeve, Sven, Gabriels, Ralf

“…Abstract Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially…”
Get full text

MS2Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 by Buur, Louise M., Declercq, Arthur, Strobl, Marina, Bouwmeester, Robbin, Degroeve, Sven, Martens, Lennart, Dorfer, Viktoria, Gabriels, Ralf

“…Rescoring of peptide–spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need…”
Get full text

MS 2 Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0 by Buur, Louise M, Declercq, Arthur, Strobl, Marina, Bouwmeester, Robbin, Degroeve, Sven, Martens, Lennart, Dorfer, Viktoria, Gabriels, Ralf

“…Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need…”
Get full text

FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data by Koutrouli, Mikaela, Nastou, Katerina, Piera Líndez, Pau, Bouwmeester, Robbin, Rasmussen, Simon, Martens, Lennart, Jensen, Lars Juhl

“…Abstract Motivation Protein networks are commonly used for understanding how proteins interact. However, they are typically biased by data availability,…”
Get full text

Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows by Staes, An, Mendes Maia, Teresa, Dufour, Sara, Bouwmeester, Robbin, Gabriels, Ralf, Martens, Lennart, Gevaert, Kris, Impens, Francis, Devos, Simon

“…Data-independent acquisition (DIA) has become a well-established method for MS-based proteomics. However, the list of options to analyze this type of data is…”
Get full text

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links by Siraj, Arslan, Bouwmeester, Robbin, Declercq, Arthur, Welp, Luisa, Chernev, Aleksandar, Wulf, Alexander, Urlaub, Henning, Martens, Lennart, Degroeve, Sven, Kohlbacher, Oliver, Sachsenberg, Timo

“…In protein‐RNA cross‐linking mass spectrometry, UV or chemical cross‐linking introduces stable bonds between amino acids and nucleic acids in protein‐RNA…”
Get full text

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling by Bouwmeester, Robbin, Richardson, Keith, Denny, Richard, Wilson, Ian D., Degroeve, Sven, Martens, Lennart, Vissers, Johannes P.C.

“…The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and…”
Get full text