This paper describes a method for proteomic analysis with applications to diagnostics and vaccines. A panel of N (⪢1) reagents called X(j), with j=1 to N, is used. The binding strength of each of the X(j) reagents to each other is measured, for example by an ELISA assay, giving an N×N matrix K. The matrix K is used to define another set of N reagents called Y(j), with j=1 to N, each of which is a linear combination of the X(j) reagents and each of which is tailored to be complementary to one of the X(j) reagents. Each of the N pairs of reagents X(j) and Y(j) defines an axis in an N-dimensional shape space. The definition of these axes facilitates proteomic analysis of diverse biological samples, for example, mixtures of proteins such as serum samples or T cell extracts. A method for defining and measuring similarity between pairs of biological samples and between sets of biological samples in the context of the set of N reagent pairs is described. This leads to methods for using the N reagent pairs in the diagnosis of diseases and in the formulation of preventive and therapeutic vaccines. The relationship of this work to previous research on shape space is discussed.
Proteomic analyser with applications to diagnostics and vaccines