XGlycScan was originally built to accept in-house data formats and a few other search-engine dependent (may or may not be proprietary) formats. However, to facilitate its general community utility and adaptability to user specific work-flows, this version and subsequent upgrades will henceforth (foremost) be made to accept the community-defined and accepted data formats. Allowances would be made occasionally for common in-house formats and other formats as requested by popular-demand.
In this version, PSMPeptide "probability" attribute is referred to as an evaluation value - a better way to describe its function. With subsequent implementations, peptides (glycopeptides) are envisaged to be evaluated not only based on probability but also based on a user-defined or specified variable. This is anticipated to make XGlycScan as robust enough as to accommodate results from differs search engines - given that various search engines score peptides in differs ways.