DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

Abstract

We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data analysis workflows that offers ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section (CCS) calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation; algorithm implementations simultaneously utilize all dimensions to (i) offer greater separation between features, thus improving detection sensitivity, (ii) increase alignment/feature matching confidence among data sets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS metabolomics data to illustrate the advantages of a multidimensional approach in each data processing step.

PyC2MC: An Open-Source Software Solution for Visualization and Treatment of High-Resolution Mass Spectrometry Data

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“…High-resolution mass spectrometry (HR-MS) has become a staple tool for biological and biomedical applications due to its high qualitative and quantitative capabilities. Benchtop HR-MS systems like the Orbitrap have had immense success in helping researchers identify ions generated from complex biological samples. − Higher identification rates as well as chemical composition monitoring can be achieved when HR-MS is coupled to liquid chromatography (LC) and the data are analyzed by sophisticated data informatics tools. − More recently, HR-MS has been coupled to ion mobility spectrometry (IMS) to aid in the differentiation of structural isomers. , Furthermore, IMS separations performed at greater than 200 resolving power have shown potential for precisely measuring ion collision cross sections (CCSs). , CCS measurements along with exact mass measurements (which provide molecular formula) and fragmentation can provide useful information about the structures of unknown ions in complex biological mixtures.…”

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