#16 · Proteomics

Software tools for peptide matching, PROTOMAP visualization and cross-link origin

The common thread is packaging computational methods into accessible, reusable software for proteomics and peptide analysis. PepHammer, a lightweight web tool, matches up to 10,000 peptides against bioactivity and tissue databases using Hamming, Grantham, and exact or partial matching. PeptideVisualizer, an open-source tool, visualizes MaxQuant peptide data, gel migration, and UniProt features for PROTOMAP analysis. XLinkDB is extended with a site confidence score that combines SASD, solvent accessibility, and salt bridges to assess the structural origin of identified cross-links across PDB structures. What is new lies mainly in packaging and scope rather than in novel matching or visualization algorithms, which the items describe as applied approaches. The cross-link confidence score is the one item adding a new analytical quantity, although its validation details are not given in the item summary.