Characterizing the chemicals within individual cells is an important analytical capability, with mass spectrometry (MS) being one of the most chemically information-rich techniques available. There are two major approaches for characterizing single cells using MS: the assay of small-volume solutions using electrospray ionization and, the focus of this chapter, measurement of cells dispersed across a surface using matrix-assisted laser desorption/ionization (MALDI) MS. In combination with spatiometric information obtained via optical imaging tools to locate individual cells on the sampling surface, follow-up measurement via MALDI MS can profile a multitude of single cells in a high-throughput manner. Compared to conventional MS imaging of the entire sample-containing surface, preselection of accurate cell locations for targeted analysis increases selectivity and throughput as well as reduces overall data size. As a result, more informative data sets are produced in less time with fewer resources. Employing this strategy, we present a multistage protocol for optical image-guided, high-throughput single cell analysis by MALDI MS. We outline steps for the isolation and preparation of single cells prior to dispersing on a glass slide for optical imaging, automated mapping of imaged cell locations using microMS, preparing the cells for MALDI MS analysis using standards and MALDI matrices, acquisition of mass spectra from mapped individual cells, and data processing and statistical analysis. Images obtained via a range of microscopy modalities can be assessed by the microMS custom image processing software suite to determine location coordinates for cells with defined morphological and/or biochemical characteristics. Depending on the biological model and MS instrumentation used, this strategy can be further enhanced by hyphenation of different imaging modalities, e.g., electron microscopy, for multidimensional sample characterization.

Original languageEnglish (US)
Title of host publicationNeuromethods
PublisherHumana Press Inc.
Number of pages49
StatePublished - 2022

Publication series

ISSN (Print)0893-2336
ISSN (Electronic)1940-6045


  • High throughput
  • Mass spectrometry
  • Matrix-assisted laser desorption/ionization
  • MicroMS
  • Microanalysis
  • Pancreatic islets
  • Peptides
  • Single cell

ASJC Scopus subject areas

  • Psychiatry and Mental health
  • General Pharmacology, Toxicology and Pharmaceutics
  • General Biochemistry, Genetics and Molecular Biology
  • General Neuroscience


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