Drug resistance emergence is a common problem that limits long term outcome benefits in the era of precision cancer therapy. Recently, we identified an early precision drug escape mechanism with adaptive tumor cellular reprogramming emerging within days after drug initiation (Fan W et al., 2011). Here we present a mass spectrometry imaging (MSI) approach to interrogate the biomolecular changes occurring within residual tumor cells under precision treatment with ALK-specific kinase inhibitor treatments in EML4-ALK fusion (ALK+) lung adenocarcinoma xenograft as well as in an ALK+ patient biopsy-derived cell line.