{"title":"MSIGen: An Open-Source Python Package for Processing and Visualizing Mass Spectrometry Imaging Data.","authors":"Emerson Hernly, Hang Hu, Julia Laskin","doi":"10.1021/jasms.4c00178","DOIUrl":null,"url":null,"abstract":"<p><p>Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS<sup>2</sup> and MS<sup>3</sup> modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS<sup>1</sup>, MS<sup>2</sup>, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1000,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of the American Society for Mass Spectrometry","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/jasms.4c00178","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/9/2 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Mass spectrometry imaging (MSI) provides information about the spatial localization of molecules in complex samples with high sensitivity and molecular selectivity. Although point-wise data acquisition, in which mass spectra are acquired at predefined points in a grid pattern, is common in MSI, several MSI techniques use line-wise data acquisition. In line-wise mode, the imaged surface is continuously sampled along consecutive parallel lines and MSI data are acquired as a collection of line scans across the sample. Furthermore, aside from the standard imaging mode in which full mass spectra are acquired, other acquisition modes have been developed to enhance molecular specificity, enable separation of isobaric and isomeric species, and improve sensitivity to facilitate the imaging of low abundance species. These methods, including MS/MS-MSI in both MS2 and MS3 modes, multiple-reaction monitoring (MRM)-MSI, and ion mobility spectrometry (IMS)-MSI have all demonstrated their capabilities, but their broader implementation is limited by the existing MSI analysis software. Here, we present MSIGen, an open-source Python package for the visualization of MSI experiments performed in line-wise acquisition mode containing MS1, MS2, MRM, and IMS data, which is available at https://github.com/LabLaskin/MSIGen. The package supports multiple vendor-specific and open-source data formats and contains tools for targeted extraction of ion images, normalization, and exportation as images, arrays, or publication-style images. MSIGen offers multiple interfaces, allowing for accessibility and easy integration with other workflows. Considering its support for a wide variety of MSI imaging modes and vendor formats, MSIGen is a valuable tool for the visualization and analysis of MSI data.
期刊介绍:
The Journal of the American Society for Mass Spectrometry presents research papers covering all aspects of mass spectrometry, incorporating coverage of fields of scientific inquiry in which mass spectrometry can play a role.
Comprehensive in scope, the journal publishes papers on both fundamentals and applications of mass spectrometry. Fundamental subjects include instrumentation principles, design, and demonstration, structures and chemical properties of gas-phase ions, studies of thermodynamic properties, ion spectroscopy, chemical kinetics, mechanisms of ionization, theories of ion fragmentation, cluster ions, and potential energy surfaces. In addition to full papers, the journal offers Communications, Application Notes, and Accounts and Perspectives