Bioinformatics

Generating high-quality libraries for DIA datasets
Lecture: Generating high-quality predicted libraries for DIA dataset peptide detection
Nov 15, 2022
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Generating high-quality libraries for DIA datasets
MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in …
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MS²Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates
Enabling novel and challenging proteomics workflows with MS²Rescore
Talk at the 2022 online EuPA Early-Career Researchers Day on MS²Rescore applications
Jun 26, 2022
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Enabling novel and challenging proteomics workflows with MS²Rescore
Machine learning to the rescue: Enabling novel proteomics workflows with data-driven bioinformatics methods
Introduction to proteomics, mass spectrometry, and machine learning for a layman audience and a summary of my PhD projects
May 19, 2022
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Machine learning to the rescue: Enabling novel proteomics workflows with data-driven bioinformatics methods
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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Algorithms for automatic spectrum identification
Lecture: Introduction to proteomics identification search engines
Sep 14, 2021
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Algorithms for automatic spectrum identification
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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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
Abstract Data-independent acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of …
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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries
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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