rIDIMS: A Novel Tool For Processing Direct-Infusion Mass Spectrometry Data

Metabolomics using mass spectrometry-only (MS) analysis either by continuous or intermittent direct infusion (DIMS) and ambient ionization techniques (AMS) has grown in popularity due to their rapid, high-throughput nature and the advantage of performing fast analysis with minimal or no sample pretr...

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Bibliographic Details
Published in:	Talanta (Oxford) Vol. 284; p. 127273
Main Authors:	Mansoldo, Felipe R.P., Lopes de Lima, Iasmim, Pais de Carvalho, Caroline, da Silva, Adriano R.J., Eberlin, Marcos Nogueira, Vermelho, Alane Beatriz
Format:	Journal Article
Language:	English
Published:	Elsevier B.V 01-03-2025
Subjects:	ambient ionization Direct Infusion mass spectrometry Graphical user interface for mass spectrometry data processing MasSpec Pen Metabolomics MasSpec Pen Direct Infusion mass spectrometry Metabolomics Graphical user interface for mass spectrometry data processing ambient ionization
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Summary:	Metabolomics using mass spectrometry-only (MS) analysis either by continuous or intermittent direct infusion (DIMS) and ambient ionization techniques (AMS) has grown in popularity due to their rapid, high-throughput nature and the advantage of performing fast analysis with minimal or no sample pretreatments. Currently, end-users without programming knowledge do not find applications with Graphical User Interface (GUI) specialized in processing DIMS or AMS data. Specifically, there is a lack of standardized workflow for processing data from limited sample sizes and scans from different total ion chronograms (TIC).To address this gap, we present rIDIMS, a user-friendly, browser-based application that offers a straightforward and fast workflow focusing on high-quality scan selection, grouping of isotopologues and adducts, data alignment, binning, and filtering. We also introduce a novel function for selecting TIC scans that is reproducible and statistically reliable, which is a feature particularly useful for studies with limited sample sizes. After processing in rIDIMS, the result is exported in an HTML report document that presents publication-quality figures, statistical data and tables, ready to be customized and exported. We demonstrate rIDIMS functionality in two cases from different areas: (i) Classification of coffee bean species through the chemical profile obtained with Mass Spec Pen; (ii) Public repository DIMS data from lipid profiling in monogenic insulin resistance syndromes. We show that our implementation facilitates the processing of AMS and DIMS data through an easy and intuitive interface, contributing to reproducible and reliable metabolomic investigations. rIDIMS is a user-friendly GUI based Shiny web application for intuitive use by end-users (available at https://github.com/BioinovarLab/rIDIMS). [Display omitted] •rIDIMS is a application with Graphical User Interface for processing DIMS/AMS data.•Fast workflow focusing on high-quality scan selection, data alignment, and filtering.•New feature particularly useful for studies with limited sample sizes.•Generation of HTML report with publication-quality figures and statistical data.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0039-9140 1873-3573 1873-3573
DOI:	10.1016/j.talanta.2024.127273