With the advent of targeted agents, it has become clinically important to distinguish histologic types of non-small cell
lung cancers (NSCLCs) using biopsy samples. We investigated whether direct tissue matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) analysis on lipid may classify histology of NSCLCs. Twentyone
pairs of frozen, resected NSCLCs were analyzed using histology-directed, MALDI MS. 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells
to identify lipid profiles, and mass spectra were acquired using a MALDI-time of flight instrument. Squamous cell
carcinomas and adenocarcinomas, two major histologic types of NSCLC, were found to have different lipid profiles.
Discriminatory lipids correctly classified the histology of 80.4% of independent NSCLC surgical tissue samples (41 out
of 51) in validation set, suggesting that lipid profiles can classify NSCLCs according to the histologic type. We also
found that protein and lipid MALDI MS profiles can classify 30 breast cancers according to the intrinsic subtypes.
Immunohistochemistry-defined, luminal, HER2+, and triple-negative tumors demonstrated different protein and lipid
profiles, as evidenced by cross validation P values < 0.01. Discriminatory proteins and lipids classified tumors according
to the intrinsic subtype with median prediction accuracies of 80.0-81.3% in 100 random test sets. Potential advantages of this label-free approach may include small tissue requirement, relatively rapid procedure, and low reagent cost. Day-today variation of this technology is also acceptable, with the Pearson correlation of 0.95. Taken together, these results suggest the possible clinical utility of histology-directed, lipid and protein MALDI MS.