GlycoViz: A glycoproteomics tool for validating and visualizing glycopeptide identifications.

SUMMARY: GlycoViz is an open-source algorithm and software tool designed to address critical bottlenecks in the post-identification workflow of mass spectrometry-based glycoproteomics. Current glyco search engines excel at glycopeptide identification but there is a lack of tools for robust post-identification validation, global glycan composition statistics, and reliable site-specific analysis, particularly concerning false positives and quantification distortion due to shallow detection depth. GlycoViz offers an alternative solution with a novel glycopeptide validation algorithm that is compatible with data from multiple search engines. Analysis of N-linked glycans is fully supported whereas O-linked glycan data analysis is limited primarily to visualization and non-optimized validation. AVAILABILITY: The open-source software is available on GitHub at https://github.com/calico/glycoviz. It can be launched as local software through Docker Compose or hosted as a web application in a server. A snapshot of the code is available on Zenodo: https://doi.org/10.5281/zenodo.22680123. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.