TRACES: A Lightweight Browser for Liquid Chromatography-Multiple Reaction Monitoring-Mass Spectrometry Chromatograms

In targeted metabolomic analysis using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS), hundreds of MRMs are performed in a single run, yielding a large dataset containing thousands of chromatographic peaks. Automation tools for processing large MRM datasets have bee...

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Bibliographic Details
Published in:Metabolites 2022-04, Vol.12 (4), p.354
Main Authors: Kita, Yoshihiro, Tokuoka, Suzumi M, Oda, Yoshiya, Shimizu, Takao
Format: Article
Language:English
Subjects:
Algorithms
Automation
Browsing
Chromatography
Datasets
deisotoping
Ions
LC-MRM-MS
Libraries
Liquid chromatography
Mass spectrometry
Mass spectroscopy
Metabolomics
Phospholipids
Proteomics
Retention
Scientific imaging
software
Software packages
targeted lipidomics
targeted metabolomics
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Summary:In targeted metabolomic analysis using liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS), hundreds of MRMs are performed in a single run, yielding a large dataset containing thousands of chromatographic peaks. Automation tools for processing large MRM datasets have been reported, but a visual review of chromatograms is still critical, as real samples with biological matrices often cause complex chromatographic patterns owing to non-specific, insufficiently separated, isomeric, and isotopic components. Herein, we report the development of new software, TRACES, a lightweight chromatogram browser for MRM-based targeted LC-MS analysis. TRACES provides rapid access to all MRM chromatograms in a dataset, allowing users to start ad hoc data browsing without preparations such as loading compound libraries. As a special function of the software, we implemented a chromatogram-level deisotoping function that facilitates the identification of regions potentially affected by isotopic signals. Using MRM libraries containing precursor and product formulae, the algorithm reveals all possible isotopic interferences in the dataset and generates deisotoped chromatograms. To validate the deisotoping function in real applications, we analyzed mouse tissue phospholipids in which isotopic interference by molecules with different fatty-acyl unsaturation levels is known. TRACES successfully removed isotopic signals within the MRM chromatograms, helping users avoid inappropriate regions for integration.
ISSN:2218-1989
2218-1989
DOI:10.3390/metabo12040354