PELSA-Decipher: A Software Tool for the Processing and Interpretation of Ligand–Protein Interaction Data Sets Acquired by PELSA

Understanding
protein–ligand interactions is fundamental
to life sciences, including the elucidation of drug action mechanisms
and regulatory processes in cellular metabolism and signaling. Recently,
a robust ligand modification-free method, termed peptide-centric local
stability assay (PELSA), has been developed to identify the protein
targets and binding regions of diverse ligands at the proteome scale.
This method has unprecedented sensitivity and can be broadly applied
to ligands such as drugs, metabolites, metal ions, antibodies, and
others. However, extracting key information on ligand–protein
interactions, including the binding proteins, binding sites, and binding
affinities, is a nontrivial task, which has limited the widespread
adoption of the PELSA strategy by the research community. To address
this, we developed a software tool, PELSA-Decipher, to facilitate
the efficient processing of data sets obtained in the PELSA experiment,
including raw data processing, result visualization, and the generation
of reports and high-quality images, thereby greatly promoting the
broader applications of the PELSA strategy. The PELSA-Decipher software
can be downloaded free of charge from the Web site https://github.com/DICP-1809/PELSA-Decipher.