Analyzing isolated collagen gel samples of a rat-tail and bovine hide, we demonstrated in situ detection of spectrally deconvoluted auto-cathodoluminescence signatures of specific molecular content with precise spatial localization over a maximum field of view of 300 µm. Correlation of the secondary electron and the hyperspectral images proved ~40 nm resolution in the optical channel, obtained due to a short carrier diffusion length, suppressed by fibril dimensions and poor electrical conductivity specific to their organic composition. By correlating statistically analyzed auto-cathodoluminescence with a mass spectroscopy data, we differentiated spectral signatures of two extracellular matrix networks - human fibrin complex and rat tail collagen isolate, and uncovered differences in protein distributions of isolated extracellular matrix networks of heterogeneous populations. Furthermore, we demonstrated how cathodoluminescence can monitor progress of a cell-remodeling process from a rat collagenous into human collagenous gel, revealing changes in complex heterogeneous biological composition confirmed by mass spectroscopy.