Proteomics

MS²DIP: Highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Accurate MS2 spectrum predictions enable drastic improvements in peptide identification workflows. This identification improvement is …
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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
The inclusion of peptide retention time prediction promises to remove peptide identification ambiguity in complex liquid …
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Algorithms for automatic spectrum identification
Lecture: Introduction to proteomics identification search engines
Sep 14, 2021
Slides DOI
Algorithms for automatic spectrum identification
Universal Spectrum Identifier for mass spectra
Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is …
DOI
Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection
Discovery of variant peptides such as a single amino acid variant (SAAV) in shotgun proteomics data is essential for personalized …
DOI
Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, …
Bart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche, Pathmanaban Ramasamy, Sigrid Verhelst, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Peter Judak, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet Debyser, Ruben t’Kindt, Koen Sandra, Surya Gupta, Nicolas Drouin, Amy Harms, Thomas Hankemeier, Donald JL Jones, Pankaj Gupta, Dan Lane, Catherine S Lane, Said El Ouadi, Jean-Baptiste Vincendet, Nick Morrice, Stuart Oehrle, Nikunj Tanna, Steve Silvester, Sally Hannam, Florian C Sigloch, Andrea Bhangu-Uhlmann, Jan Claereboudt, N Leigh Anderson, Morteza Razavi, Sven Degroeve, Lize Cuypers, Christophe Stove, Katrien Lagrou, Geert A Martens, Dieter Deforce, Lennart Martens, Johannes PC Vissers, Maarten Dhaenens
DOI
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13th to January …
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The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows
A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include …
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The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows
The HUPO-PSI standardized spectral library format
More and more proteomics datasets are becoming available in public repositories. The knowledge embedded in these datasets can be used …
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MS²PIP: Predicting peptide spectrum peak intensities to improve proteomics identification
Jul 18, 2019
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