GlyCombo works best with mzML input as it enables the output of three files. The first is a csv file which includes glycan compositions matches, mass error of the matches, and the scan number of the respective MS2 spectrum. The second is a similar csv file which has additional columns enabling direct import into tools which generate extracted ion chromatograms (EIC) such as Skyline (an example is provided in Supplementary Table ). The final file is a parameters file, giving the specific parameters used to generate the given output, as well as the list of precursors searched. In this work, we have used this list of precursors to benchmark our platform against one of the most popular approaches for glycan composition identification, GlycoMod. Users are also given the ability to use a text-based list of glycan masses within the GUI. In this case, the output is limited to a csv file which includes the glycan composition matches and mass error of the matches.