To construct a diagnostic algorithm for tumour areas stimulated with TGF-β1 in HNSCC, we acquired a total of 240 and 90 mass spectra from human recombinant TGF-β1-stimulated or -unstimulated human HNSCC cells, respectively, using both the positive- and negative-ion modes, and then logistic regression (LR) was used for discrimination analysis as a diagnostic algorithm. Here, TGFB1 is linked to head and neck squamous cell carcinoma.