sample-preparation-for-single-cell-mass-spectrometry-metabolomics

Sample Preparation for Single Cell Mass Spectrometry Metabolomics Studies: Combined Cell Washing, Quenching, Drying, and Storage

Single-cell mass spectrometry (SCMS) has become an indispensable tool for studying cellular metabolism. Owing to advancements in modern mass spectrometry ...

single-cell-mass-spectrometry-imaging-using-desorption-electrospray

Single-Cell Mass Spectrometry Imaging Using Desorption Electrospray Ionization Coupled To Orbitrap Mass Spectrometers

Desorption electrospray ionization&#8211;mass spectrometry imaging (DESI&#8211;MSI) enables ambient, matrix-free molecular imaging with minimal sample ...

University of Oklahoma

University of Oklahoma Health Campus

Mass spectrometry (MS) has been one of the most widely used tools for bioanalytical analysis due to its high sensitivity, capability of quantitative analysis, and compatibility with biomolecules. Among various MS techniques, single cell mass spectrometry (SCMS) is an advanced approach to molecular analysis of cellular contents in individual cells. In tandem with the creation of novel experimental techniques, the development of new SCMS data analysis tools is equally important. As most published software packages are not specifically designed for pretreatment of SCMS data, including peak alignment and background removal, their applicability on processing SCMS data is generally limited. Hereby we introduce a Python platform, MassLite, specifically designed for rapid SCMS metabolomics data pretreatment. This platform is made user-friendly with graphical user interface (GUI) and exports data in the forms of each individual cell for further analysis. A core function of this tool is to use a novel peak alignment method that avoids the intrinsic drawbacks of traditional binning method, allowing for more effective handling of MS data obtained from high resolution mass spectrometers. Other functions, such as void scan filtering, dynamic grouping, and advanced background removal, are also implemented in this tool to improve pretreatment efficiency.

MassLite: An integrated python platform for single cell mass spectrometry metabolomics data pretreatment with graphical user interface and advanced peak alignment method.

The Single-probe single-cell mass spectrometry (SCMS) is an innovative analytical technique designed for metabolomic profiling, offering a miniaturized, multifunctional device capable of direct coupling to mass spectrometers. It is an ambient technique leveraging microscale sampling and nanoelectrospray ionization (nanoESI), enabling the analysis of cells in their native environments without the need for extensive sample preparation. Due to its miniaturized design and versatility, this device allows for applications in diverse research areas, including single-cell metabolomics, quantification of target molecules in single cell, MS imaging (MSI) of tissue sections, and investigation of extracellular molecules in live single spheroids. This review explores recent advancements in Single-probe-based techniques and their applications, emphasizing their potential utility in advancing MS methodologies in microscale bioanalysis.

Exploring Single-Probe Single-Cell Mass Spectrometry: Current Trends and Future Directions.

Single-cell mass spectrometry (SCMS) has emerged as a powerful tool for analyzing metabolites in individual cells, including live cells. However, cell metabolites have a rapid turnover rate, whereas maintaining metabolites' profiles of live cells during sample transport, storage, or extended measurements can be challenging. In this study, a cell preparation method, which integrates cell washing by volatile salt solution, rapid liquid nitrogen (LN) quenching, freeze-drying in vacuum, and freezer storage at -80 °C, to preserve cell metabolites for SCMS measurement is discussed. Experimental results revealed that LN quenching preserved the overall cell metabolome, whereas storage at -80 °C for 48 h slightly changed the metabolite profiles in quenched cells. However, metabolites in unquenched cells were changed regardless of low-temperature storage. The influence of omission of quenching and low-temperature storage on cell metabolites and relevant pathways were investigated. Results from this work indicate that cell quenching is necessary, but low-temperature storage time should be minimized to preserve cell metabolites. The method developed in the current work can be readily adopted by SCMS techniques with storage remaining largely unaltered, allowing for extended SCMS studies.

ArticleTotal : 2	Year
Publication title Cited by 1	2025
Publication title	2026

Article	Year
MassLite: An integrated python platform for single cell mass spectrometry metabolomics data pretreatment with graphical user interface and advanced peak alignment method. Analytica chimica acta\| PubMed ID: 39244309	2024
Exploring Single-Probe Single-Cell Mass Spectrometry: Current Trends and Future Directions. Analytical chemistry\| PubMed ID: 39999987	2025
Developing a Cell Quenching Method to Facilitate Single Cell Mass Spectrometry Metabolomics Studies. JACS Au\| PubMed ID: 40443889	2025

Deepti Bhusal

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