aimed analytics logo

Innovations in Single-Cell Multiomics Through Mass Spectrometry

Dive into the forefront of biological discovery with our latest highlight on a recent review: the breakthroughs in mass spectrometry-enabled multiomics at the single-cell level. Unveil the future of understanding complex cellular mechanisms and the revolutionary potential of single-cell analysis to transform life sciences. Get ready for a glimpse into the microscopic world like never before.

Harnessing the Power of Mass Spectrometry for Single-Cell Multiomics Analysis

Biological systems are remarkably complex, with myriad processes occurring simultaneously within and across cells. Understanding these systems demands a detailed examination of the molecular changes that occur in response to various stimuli. Mass spectrometry (MS) has emerged as a critical tool in this endeavor, especially when combined with other analytical techniques for multiomic analysis at the single-cell level.

This article delves into the recent advancements in MS-enabled multiomics, shedding light on the potential of these technologies to unravel the intricacies of biological organisms.

Introduction to Mass Spectrometry in Single-Cell Analysis

The study of health and disease at the molecular level requires a systems-level approach, examining the interplay between genes, transcripts, proteins, and metabolites. Traditional bulk analyses, while useful, often overlook the heterogeneity of cell populations and the presence of rare but biologically significant cells.

This gap has led to the development of novel single-cell -omic techniques supported by initiatives like the Human Biomolecular Atlas Program (HuBMAP) and the Human Cell Atlas. Single-cell RNA sequencing (scRNAseq) techniques have revolutionized our understanding of biological processes, but they fall short in measuring proteins and metabolites/lipids directly. This is where mass spectrometry (MS) shines, offering the sensitivity, robustness, and flexibility needed to analyze a wide range of biomolecules.

Advancements in Single-Cell Multiomics

Recent technological advances in MS have enabled researchers to perform both cellular and subcellular analyses, categorizing techniques into in situ and ex situ MS-enabled single-cell multiomics

  • In Situ Techniques: These include MS imaging (MSI), which retains the spatial context by analyzing biomolecules directly from thin tissue sections. MALDI (Matrix-Assisted Laser Desorption/Ionization) is a versatile tool in this category, used for analyzing proteins, peptides, lipids, and metabolites, among others. 

  • Ex Situ Techniques: These involve removing single cells from their spatial context, often requiring chromatographic separations before MS analysis. Ex situ techniques face challenges such as analyte loss but have been bolstered by microfluidic techniques and improvements in MS sensitivity.

One notable study highlighted in this review combines non-targeted MALDI-MSI with fluorescence in situ hybridization (FISH) to explore the symbiotic relationships between deep-sea mussels and their intracellular bacteria. This approach exemplifies the power of combining MS with orthogonal techniques for a more comprehensive understanding of biological systems.

It is also noteworthy that no studies have yet accomplish measuring all three major classes of biomolecules in a non-targeted manner from the same single-cell using MS methods alone or in combination with other methods
Kumar et al. (2024): Advances in mass spectrometry-enabled multiomics at single-cell resolution. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-gmw9l

The Future of MS-Enabled Multiomics

Despite the strides made in MS-enabled multiomics, the field is still in its nascent stages. The review posits, "It is also noteworthy that no studies have yet accomplished measuring all three major classes of biomolecules in a non-targeted manner from the same single-cell using MS methods alone or in combination with other methods."

This highlights the potential for future research to further integrate and optimize these techniques for comprehensive single-cell analysis.


The integration of mass spectrometry with single-cell analysis techniques represents a significant leap forward in our ability to understand complex biological systems. By enabling the measurement of multiple biomolecular modalities from the same cells or tissue sections, researchers can gain insights into the dynamic changes occurring within and across cells.

As the field continues to evolve, we can expect to see novel discoveries that deepen our understanding of health, disease, and the fundamental processes of life.

As we continue to peel back the layers of cellular complexity, the integration of mass spectrometry with single-cell multiomics not only offers a glimpse into the uncharted territories of biological systems but also promises to pave the way for personalized medicine and targeted therapies.

By enabling an unprecedented level of detail in our understanding of cellular functions and interactions, these advancements signal a new era in scientific inquiry where the mysteries of life at the molecular level can be deciphered with greater precision and clarity. The journey into the microscopic realm is just beginning, and the insights gained from these pioneering studies will undoubtedly shape the future of biomedical research and beyond.