Resolving sialylated N Glycans and immune cell landscapes using a unified same-section IMC-MSI workflow

Integrating antibody-based imaging with mass spectrometry imaging (MSI) on the same formalin-fixed paraffin-embedded (FFPE) tissue section offers powerful opportunities for multimodal spatial analysis but remains analytically challenging due to cross-platform chemical and physical interference. In particular, chemically aggressive on-tissue derivatization strategies required for isomer-resolved glycan MSI may compromise downstream antibody detection. Here, we systematically evaluate the analytical compatibility and acquisition order of imaging mass cytometry (IMC) and sialic-acid-linkage-resolving N-glycan MALDI-MSI using an Amidation-Activation-X-Linkage (AAXL) derivatization strategy on the same FFPE tissue section. Two same-section workflows were compared: AAXL-MALDI MSI followed by IMC (MALDI-first) and IMC followed by AAXL-MALDI MSI (IMC-first). We find that AAXL-first processing results in severe and widespread loss of IMC anti-body signal across epithelial, immune, and nuclear markers, rendering subsequent antibody-based analysis unreliable. In contrast, IMC-first acquisition preserves quantitative antibody performance while maintaining spatial glycan distributions, relative abundance structure, and isomer-specific signal integrity in downstream AAXL-MALDI MSI. Using high-precision co-registration, we further demonstrate that IMC-first sequencing enables analytically robust integration of IMC and MSI data at both domain and pixel levels. These results establish IMC-first acquisition as the preferred same-section strategy for workflows combining antibody imaging with chemically intensive, isomer-resolved glycan MSI and provide generalizable guidance for the design of multimodal spatial mass spectrometry experiments.