4.7 Article

Data-Driven and Machine Learning-Based Framework for Image-Guided Single-Cell Mass Spectrometry

Journal

JOURNAL OF PROTEOME RESEARCH
Volume 22, Issue 2, Pages 491-500

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.2c00714491J

Keywords

single-cell analysis; mass spectrometry; data-driven analysis; machine learning

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Improved throughput and enhanced detection limits enable researchers to characterize the functional states of individual cells using single-cell chemical analysis. Image-guided single-cell mass spectrometry combines optical microscopy and fluorescence microscopy to analyze cellular and subcellular targets. In this study, a data-driven and machine learning workflow called DATSIGMA was proposed for feature extraction and interpretability of complex single-cell mass spectrometry data. The toolset was successfully implemented and tested on various experimental data sets, showing its potential for diverse biological applications.
Improved throughput of analysis and lowered limits of detection have allowed single-cell chemical analysis to go beyond the detection of a few molecules in such volume-limited samples, enabling researchers to characterize different functional states of individual cells. Image-guided single-cell mass spectrom-etry leverages optical and fluorescence microscopy in the high-throughput analysis of cellular and subcellular targets. In this work, we propose DATSIGMA (DAta-driven Tools for Single-cell analysis using Image-Guided MAss spectrometry), a workflow based on data-driven and machine learning approaches for feature extraction and enhanced interpretability of complex single-cell mass spectrometry data. Here, we implemented our toolset with user-friendly programs and tested it on multiple experimental data sets that cover a wide range of biological applications, including classifying various brain cell types. Because it is open-source, it offers a high level of customization and can be easily adapted to other types of single-cell mass spectrometry data.

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