Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

Researchers develop a methylamine-based method that nearly eliminates peptide overlabeling in proteomics, improving accuracy in protein identification and quantitation.

Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

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The Wellcome Trust gives Discovery Award to Professor Matt Higgins to support his "Molecular mechanisms of erythrocyte invasion in malaria" research

Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...

Proteins exist in multiple conformations or states, often associated with different functional capacities. The ability to selectively identify and study these states is crucial for under-standing the ...

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Scientists can choose between multiple human genome references, and a pangenome reference is coming. Deciding what to use when is not quite straightforward.

In attempting to observe the behaviour of a protein of interest in vivo, akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or ...

Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution. However, current isolation procedures for peptide-RNA crosslinks eliminate the RNA moiety, prohibiting sequencing of the RNA alongside the crosslinked peptide. Here, we introduce peptide-RNA crosslink isolation for sequencing by mass spectrometry or pepR-MS, a method that enriches peptide-RNA crosslinks with RNA chains of tunable length. Applied to breast cancer cells, pepR-MS identifies over 21,000 unique crosslinks at 4,757 crosslinking sites in 744 proteins. Employing different nucleases, we capture crosslinks with RNA moieties up to six nucleotides, revealing RNA crosslinking preferences at domain and subdomain resolution. Finally, we demonstrate mass spectrometry-based sequential sequencing of both peptide and RNA from the same crosslink, providing a starting point for the analysis of long-chain peptide-RNA crosslinks that map interaction interfaces across the proteome and transcriptome.