Title:	Target and nontarget LC_qTof analysis computation
DNr:	LiU-compute-2025-24
Project Type:	LiU Compute
Principal Investigator:	Thanh Duc Nguyen <thanh.duc.nguyen@liu.se>
Affiliation:	Linköpings universitet
Duration:	2025-05-22 – 2026-01-01
Classification:	10401
Keywords:

Abstract

This project aims to develop an efficient computational workflow for processing and analyzing raw mass spectrometry data using open-source tools. The workflow begins with MSconvert ProteoWizard, which connects to our Tema M lab computer (at IP:10.161.8.10) to access raw data. These files, averaging 5 GB per data file, are converted into the mzML format, enabling further analysis. Given that each batch produces between 20 to 100 files, we are facing significant computational challenges due to the sheer volume and complexity of the data. To address these challenges, we utilize MZmine 3 for non-targeted analysis, supporting feature detection, chromatographic alignment, and visualization. For targeted analysis, we employ OpenSWATH and Skyline, both widely used for quantification and compound identification within mass spectrometry datasets. The outcomes of this workflow will directly contribute to ongoing research projects at Tema M and IFM, enhancing analytical capabilities and supporting data-driven scientific investigations.