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...

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...

Our understanding of how post-translational modification—protein phosphorylation—impacts the complexity of eukaryotic signalling pathways is continuously expanding. Now, protein oligophosphorylation h...

Targeted covalent inhibitors are powerful entities in drug discovery, but their application has so far mainly been limited to addressing cysteine residues. The development of cysteine-directed covalen...

Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...

Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...

The computational workflow of DIA-Umpire allows untargeted peptide identificationdirectly from DIA (data-independent acquisition) proteomics data without dependence on a spectral library for data extr...

Data-independent acquisition advances proteomics quantification. Here, the authors present diaTracer, a spectrum-centric tool for diaPASEF data that supports broad proteomics applications, enabling di...

Data-independent acquisition advances proteomics quantification. Here, the authors present diaTracer, a spectrum-centric tool for diaPASEF data that supports broad proteomics applications, enabling di...

Top-down proteomics has emerged as a transformative method for the analysis of protein sequence and post-translational modifications (PTMs). Top-down experiments have historically been performed prima...