Mass spectrometry imaging needs to sample point by point on a plane to obtain coordinates; three-dimensional tissue cannot be scanned directly and must be cut into thin layers to expose the cross-section. Section thickness and flatness affect the sampling consistency of laser/spray/ion beam, thereby determining pixel-to-pixel comparability.
In addition, if the sectioning process causes molecular migration or degradation, it will blur the true spatial distribution. Therefore, the sectioning process together with subsequent fixation and preservation determines the fidelity of in-situ information.
Common ones are paraffin-embedded sections and frozen sections: paraffin sections preserve morphology well but require dewaxing and may introduce solvent disturbance; frozen sections (cryo-sections) are cut at low temperature, more conducive to retaining small molecules and metabolites, and are the first choice for mass spectrometry imaging. Conductive slides can be used for vacuum sources requiring conductivity (such as TOF-SIMS).
For matrix-free ambient sources (LDPI, DPI, DESI), sampling is usually direct after sectioning or with only minimal processing; for MALDI, additional matrix spraying is required, and section quality also affects matrix uniformity.
Sectioning needs to be compatible with downstream readouts: if H&E staining or IHC morphological annotation is planned, the section should balance the operability of mass spectrometry and staining; if conductive slides are used, the matching of the target surface and ion transmission must also be considered.
Standardized sectioning SOP (thickness, temperature, blade, transfer) is the basis of cross-project comparability and should be written into the imaging experiment specification and connected with the registration workflow of analysis software.
Misconceptions include sections that are too thick causing uneven sampling penetration, thawing causing molecular migration, and knife marks introducing artifacts. Quality control can be done through optical-microscope initial inspection, matrix-uniformity checks, and known-molecular signal verification.
For imaging requiring subcellular resolution, section quality is one of the bottlenecks; in this case, a cryo-mass-spectrometry imaging source and low-temperature stable workflow must be paired to avoid sample preparation becoming the resolution ceiling.
To obtain detailed specifications, compatible models, or a quotation for the MSI LDPI / DPI full series imaging ion sources, visit the Neo-Source official website, or contact the official team for compatibility advice tailored to your mass spectrometer (Agilent / SCIEX / Thermo and other mainstream MS).