Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry

Abstract

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

Figure 1

Overview of the single-cell sampling methods covered in this Perspective. (A) Tissue may be sectioned and mounted on a suitable surface for imaging native distributions of analytes. (B) Specific large cells can be isolated from tissue for subsequent analysis. (C) Cells from tissue may be dissociated or cultured in growth medium.

Figure 2

Several MSI methods obtain single-cell resolution. (A) Application of a matrix is required for MALDI-MSI and must be optimized to maintain native spatial distributions. While spatial resolution is poorer than with SIMS, MALDI ionization is much softer, such that intact lipids and peptides are detectable. (B) SIMS provides the highest spatial resolution with focused primary ion beams but is limited in analyte coverage, typically detecting fragment ions and small compounds. (C) Imaging mass cytometry is capable of targeted localization of protein antigens with resolutions similar to SIMS.

Figure 3

Illustration of an experimental workflow utilizing CE-MS to separate and quantify endogenous molecules in single cells. Specific cell types are either (A) isolated from tissue manually or (B) chemically labeled and sorted by microfluidic devices. Each cell is homogenized or lysed, and its content is subjected to CE-MS separation and quantitation.

Figure 4

Analysis of dissociated or cultured cells provides the highest throughput of any SCMP-MS method. (A) Mass cytometry uses rare earth metal-labeled affinity tags to quantitatively measure up to hundreds of preselected antigens. The current throughput is ∼1 kHz and data can be visualized with traditional cytometry plots or multivariate analysis. Dissociated cells can also be attached to surfaces for MALDI-MS profiling within (B) microarrays for MS or randomly seeded and targeted by (C) optically guided profiling.