A method for the separation of particles of different densities using a step-wise gradient density extraction method as described herein where a sample is suspended in a liquid volume of an extracting medium of specific density and the particles that have a density less than or equal to that of the extracting medium of specific density can be recovered from a horizonatally rotatable hollow disk or a removable receptacle within a horizontally rotatable hollow disk designed for such purposes while the particles that have a density greater than the extracting medium of specific density form a deposit which can be cycled through the extraction process in an iterative fashion by varying the density of the extracting medium allowing the recovery of discrete particles of differing densities from a test sample. Also disclosed herein is the use of the above method as part of a separate method or system to identify a ratio of biomarkers from different fractions of a sample homogenate or lysate which is useful in the evaluation of potential biomarkers, and for the intraoperative pathological diagnosis of positive margins of cancer and other diseases.