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Abstract
Conventional methods of Glycosaminoglycan profiling have contributed to a lag in glycomics advancement. Single reaction monitoring is commonly employed in targeted mass spectrometry, but results in longer acquisitions and lower sample throughput, taking 30-60 minutes per run. Parallel reaction monitoring proposes a novel approach to tackling these problems. Using high-resolution Fourier Transform mass spectrometry and an open-source program Skyline for data analysis, automation of analysis process for disaccharide profiling was achieved. Initial front-end input of precursor mass, mass transitions, retention times, and retention time windows into savable template for all future analyses. Skyline provides calibration curve building and quantification, calibration, and sample spectra into preset documents. A 10-minute method for direct single-type analysis and a 20-miute method for simultaneous analysis was optimized using reverse-phase liquid chromatography. Two-fold increase in sample throughout capabilities and analysis automation revolutionizes larger scale profiling experiments and minimizes data disparity between other higher throughput omics fields.