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. Author manuscript; available in PMC: 2021 Jul 1.
Published in final edited form as: Annu Rev Biomed Data Sci. 2020 Apr 13;3:61–87. doi: 10.1146/annurev-biodatasci-011420-031537

Table 1. Imaging MS parameters and how they affect data properties.

Parameters of imaging MS Affected aspects and data properties
Sample preparation MALDI matrix (e.g., DHB, DAN) Desorption and ionization (and hence detectable molecular classes), spatial resolution (but not critically), sensitivity
Solvent (e.g., acetonitrile) Desorption and ionization, sensitivity
Source Source type (e.g., MALDI, DESI, SIMS, IR-MALDESI) Desorption and ionization, sensitivity (and thus the number of ion channels), potentially spatial resolution (and thus the number of pixels)
Analyzer Analyzer type (FTICR, Orbitrap, TOF, QTOF) Strongly affects spectral properties (dimensionality, noise, background, and, in particular, TOF) and molecular ambiguity; affects spatial properties (noise, resolution) to a lesser degree
Polarity (positive, negative) Which ions are detected (and hence molecular classes)
Mass-resolving power (e.g., 50,000 or 120,000 at 200 m/z) Critically affects molecular ambiguity (inversely proportional) and data size (proportional)
Mass accuracy Critically affects data quality, molecular ambiguity, and interpretability

Abbreviations: DAN, 1,5-diaminonapthalene; DESI, desorption electrospray ionization; DHB, 2,5-dihydroxybenzoic acid; FTICR, Fourier transformation ion cyclotron resonance; IR-MALDESI, infrared matrix-assisted laser desorption electrospray ionization; MALDI, matrix-assisted laser desorption/ionization; MS, mass spectrometry; QTOF, quadrupole time-of-flight; SIMS, secondary ion mass spectrometry; TOF, time-of-flight.