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MSE and HDMSE are LC/MS-based acquisition strategies for life sciences that can be used for a variety of research focused applications and applied to the ACQUITY UPLC System and oa-Tof-based mass spectrometry platforms, including the SYNAPT G2-S HDMS System. In LC/HDMSE-based acquisitions, ions are separated in the gas phase by ion mobility and subsequently, the energy applied to the collision cell is alternated between a low and elevated state on a scan-to-scan basis, providing both qualitative and quantitative accurate mass precursor and product ion information that is retention and drift time aligned. The challenge is to make use of the high quality ion mobility resolved data that are generated. 

This application note introduces the workflow of TransOmics Informatics Software that has been specifically developed for the larger scale analysis of ion mobility MS data from proteomics and metabolomics data sets, comprising technical and biological replicates.

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