Precise co-registration of mass spectrometry imaging, histology, and laser microdissection-based omics

Frederic Dewez, Marta Martin-Lorenzo, Michael Herfs, Dominique Baiwir, Gabriel Mazzucchelli, Edwin De Pauw, Ron M. A. Heeren, Benjamin Balluff*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Mass spectrometry imaging (MSI) is an analytical technique for the unlabeled and multiplex imaging of molecules in biological tissue sections. It therefore enables the spatial and molecular annotations of tissues complementary to histology. It has already been shown that MSI can guide subsequent material isolation technologies such as laser microdissection (LMD) to enable a more in-depth molecular characterization of MSI-highlighted tissue regions. However, with MSI now reaching spatial resolutions at the single-cell scale, there is a need for a precise co-registration between MSI and the LMD. As proof-of-principle, MSI of lipids was performed on a breast cancer tissue followed by a segmentation of the data to detect molecularly distinct segments within its tumor areas. After image processing of the segmentation results, the coordinates of the MSI-detected segments were passed to the LMD system by three co-registration steps. The errors of each co-registration step were quantified and the total error was found to be less than 13 mu m. With this link established, MSI data can now accurately guide LMD to excise MSI-defined regions of interest for subsequent extract-based analyses. In our example, the excised tissue material was then subjected to ultrasensitive microproteomics in order to determine predominant molecular mechanisms in each of the MSI-highlighted intratumor segments. This work shows how the strengths of MSI, histology, and extract-based omics can be combined to enable a more comprehensive molecular characterization of in situ biological processes.

Original languageEnglish
Pages (from-to)5647-5653
Number of pages7
JournalAnalytical and Bioanalytical Chemistry
Issue number22
Publication statusPublished - Sept 2019


  • Mass spectrometry imaging
  • Laser microdissection
  • Microproteomics
  • Co-registration
  • Intratumor heterogeneity


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