Peptide Mass Fingerprinting (PMF) is a technique used to identify proteins by matching their constituent fragment masses (peptide masses) to the theoretical peptide masses generated from a protein or DNA database. The first step in PMF is that an intact, unknown protein is cleaved with a proteolytic enzyme to generate peptides. With PMF, heterogeneity is most commonly imparted to the unknown protein with a trypsin digestion. The premise of peptide mass finger printing is that every unique protein will have a unique set of peptides and hence unique peptide masses. Identification is accomplished by matching the observed peptide masses to the theoretical masses derived from a sequence database. PMF identification relies on observing a large number of peptides, 5+, from the same protein at high mass accuracy. This technique does well with 2D gel spots where the protein purity is high. PMF protein identification can run into difficulties with complex mixtures of proteins. Low level ID also becomes difficult due to commonplace contamination by keratin.

The finite element method is a method for solving partial differential equations (PDEs). For example a PDE will involve a function u(x) defined for all x in the domain with respect to some given boundary condition. The purpose of the method is to determine an approximation to the function u(x). This method requires the discretisation of the domain into subregions or cells. For example, a two-dimensional domain can be divided and approximated by a set of triangles (the cells). On each cell the function is approximated by a characteristic form. For example u(x) can be approximated by a linear function on each triangle. The method is applicable to a wide range of physical and engineering problems. Finite element method is a powerful technique originally developed for numerical solutions of complex problems in structural mechanics, and it remains the method of choice for complex systems. In FEM, the structural system is modeled by a set of appropriate finite elements interconnected at points called nodes. Elements may have physical properties such as thickness, coefficient of thermal expansion, density, Young's modulus, shear modulus and Poisson's ratio.