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Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes
Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and …
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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
A comprehensive evaluation of consensus spectrum generation methods in proteomics
Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of …
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Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide …
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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 …
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Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide …
DOI
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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DeepLC can predict retention times for peptides that carry as-yet unseen modifications
timsTOF analysis combined with fragment intensity predictions results in improved identification of classical bioactive peptides and sORF-encoded peptides
Bioactive peptides exhibit key roles in a wide variety of complex processes, such as regulation of body weight, learning, aging, and …
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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 …
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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 …
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