 AutopiMS is a single-ion MS-based multiplexed workflow for top-down tandem MS directly from tissue microenvironments in a semi-automated manner that allows for the identification of 73. Protea forms up to 54 KDA at a rate of less than one minute per protea form, and can be interfaced with multi-faceted protea form imaging MS data modalities for the identification of protea form signatures in tumour and stromal regions in ovarian cancer biopsies. From a total of 1,000 protea forms detected by region of interest label-free quantitation, AutopiMS discovers 303 differential protea forms in stroma versus tumour from the same patient, with 14 of the top protea form signatures corroborated by MSI at 20 micron resolution including the differential localization of methylated forms of CIP1. This article was authored by John P. McGee, Pesu, Kenneth Adubin and others. We are article.tv, links in the description below.