Prediction of peptide mass spectral libraries with machine learning
J Cox - Nature Biotechnology, 2023 - nature.com
The recent development of machine learning methods to identify peptides in complex mass
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods …
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry
(MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the …
(MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the …
Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome
Immunopeptidomics is a key technology in the discovery of targets for immunotherapy and
vaccine development. However, identifying immunopeptides remains challenging due to …
vaccine development. However, identifying immunopeptides remains challenging due to …
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 chromatography–mass spectrometry identification workflows …
ambiguity in complex liquid chromatography–mass spectrometry identification workflows …
MS2Rescore: data-driven rescoring dramatically boosts immunopeptide identification rates
A Declercq, R Bouwmeester, A Hirschler… - Molecular & Cellular …, 2022 - ASBMB
Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented
peptides on almost all cells that can be used in anti-cancer vaccine development. However …
peptides on almost all cells that can be used in anti-cancer vaccine development. However …
Updated MS²PIP web server supports cutting-edge proteomics applications
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 …
been strongly on the rise over the past years, especially for applications in challenging …
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's
fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have …
fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have …
INFERYS rescoring: Boosting peptide identifications and scoring confidence of database search results
DP Zolg, S Gessulat, C Paschke… - Rapid …, 2021 - Wiley Online Library
Database search engines for bottom‐up proteomics largely ignore peptide fragment ion
intensities during the automated scoring of tandem mass spectra against protein databases …
intensities during the automated scoring of tandem mass spectra against protein databases …
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
In the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based
proteomics was unfolded with the introduction of dozens of novel instruments that …
proteomics was unfolded with the introduction of dozens of novel instruments that …
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer
H Liao, C Barra, Z Zhou, X Peng, I Woodhouse… - Nature …, 2024 - nature.com
Understanding the nature and extent of non-canonical human leukocyte antigen (HLA)
presentation in tumour cells is a priority for target antigen discovery for the development of …
presentation in tumour cells is a priority for target antigen discovery for the development of …