The identification of glycans in raw files serves as the first foundational step of glycomics data analysis. We describe a new open-source computational tool, GlyCombo, that is capable of rapidly elucidating possible glycan compositions from MS analyses. In this paper we utilize GlyCombo and benchmark its performance against the current state-of-the-art combinatorial solution for glycomics, GlycoMod. The experimental results exemplify the speed and robustness of GlyCombo for use with N-glycans, O-glycans, glycans released from glycosphingolipids, in combination with multiple polarities and derivatisation states. In addition to faster search times, broader accessibility, and completeness of annotation, processing is automated, and output are specifically formatted to connect with downstream processes including GlycoWorkBench for structural annotation, and Skyline for quality control and quantitation.