Abstract: Embodiments are directed to methods for representing cell content of a tissue sample. One method includes identifying a pixel in a digital image of a tissue sample. The identified pixel is mapped to a portion of the tissue sample. A first data set is accessed representing a genomics analysis of nucleic acids that are separated from tissue proteins in the tissue sample. A second data set is also accessed representing a proteomic analysis of proteins that were separated from the nucleic acids of the tissue sample. The data sets are mapped to a renderable attribute, so that the renderable attribute has a specified value based on the mapped data sets. Then, a portion of a representation is rendered for the identified pixel, according to the specified value of the renderable attribute. The representation includes an indication of how the separated nucleic acids and proteins are distributed within the tissue sample.

Abstract: Methods of isolating nucleic acid and protein molecules from a single formalin-fixed, paraffin-embedded (FFPE) tissue sample section include lysing the cells of the tissue sample section, alkylating, reducing, and enzymatically digesting proteins in the lysate, and separating nucleic acids present in the lysate from the digested proteins. Cell lysis is performed under conditions that permit extraction of DNA, RNA, and proteins that are suitable for genomic and proteomic analysis. In particular, the buffer conditions, reaction time, and temperature of the lysis reaction are such that a suitable amount of DNA, RNA, and proteins are released and in stable condition for separation and proteogenomic analysis. Systems for performing methods include reagents and apparatus for performing steps of the method. Panels for detecting the presence and level of expression of peptides to differentiate between disease states include a plurality of peptides.