<jats:title>Abstract</jats:title><jats:p>Tissue spray ionization mass spectrometry (TSI-MS) directly on small tissue samples has been shown to provide highly specific molecular information. In this study, we apply this method to the analysis of 38 pairs of human lung squamous cell carcinoma tissue (cancer) and adjacent normal lung tissue (normal). The main components of pulmonary surfactants, dipalmitoyl phosphatidylcholine (DPPC, <jats:italic>m/z</jats:italic> 757.47), phosphatidylcholine (POPC, <jats:italic>m/z</jats:italic> 782.52), oleoyl phosphatidylcholine (DOPC, <jats:italic>m/z</jats:italic> 808.49) and arachidonic acid stearoyl phosphatidylcholine (SAPC, <jats:italic>m/z</jats:italic> 832.43), were identified using high-resolution tandem mass spectrometry. Monte Carlo sampling partial least squares linear discriminant analysis (PLS-LDA) was used to distinguish full-mass-range mass spectra of cancer samples from the mass spectra of normal tissues. With 5 principal components and 30 – 40 Monte Carlo samplings, the accuracy of cancer identification in matched tissue samples reached 94.42%. Classification of a tissue sample required less than 1 min, which is much faster than the analysis of frozen sections. The rapid, in situ diagnosis with minimal sample consumption provided by TSI-MS is advantageous for surgeons. TSI-MS allows them to make more informed decisions during surgery.</jats:p>