PERCEPTRON-XFMS: An Open-Source Web Server for Analysis of X-ray Footprinting with Mass Spectrometry Data

PERCEPTRON-XFMS is a freely available web-based platform for automated X-ray Footprinting with Mass Spectrometry (XFMS) analysis. XFMS provides residue-specific information on protein solvent accessibility by determining hydroxyl radical modification towards investigating protein interactions and conformational changes. The approach can enable global identification of structural waters associated with surface and internal residues in a protein. Towards an integrative analysis of XFMS data, PERCEPTRON-XFMS (i) extracts and quantifies oxidation rates, (ii) computes dose-response curves, and (iii) calculates protection factors for modified residues. The webserver takes five input files: (i) LC-MS data (mzXML), (ii) Mascot search results, (iii) protein sequence (fasta), (iv) structure (PDB), and (v) solvent accessible surface area (SASA) values. The platform outputs (i) dose-response plots, (ii) protection factors, and (iii) centrality values of modified residues. For a convenient visualization of these results, the webserver also provides PDB files with protection factors, and centrality scores as an output. This is the first integrative platform that seamlessly brings together experimental and computational measures of water dynamics; thus, providing a much-needed bioinformatics tool for both fundamental and applied protein science. PERCEPTRON-XFMS webserver is freely available at https://perceptronxfms.lums.edu.pk along with its source code, at https://data.mendeley.com/datasets/ssjxhyrtwc.