This chapter evaluates the usability of known protein markers for quantitative protein profiling assays applicable to forensic and biometric applications. We will discuss the use of competitive displacement assays and peptidomics technology in the design of multiplex protein assays for laboratory-based and potentially scene-of-crime applications. Competitive displacement assays embody the most accurate multiplex protein affinity assay system to date, applicable to a wide range of protein profiling applications. The peptidomics technology is the most generic and multiplatform-compatible affinity assay system to date, applicable for protein identification, quantification and expression profiling. It relies on proteolytic protein digestion, requires only the availability of small peptide fragment(s) and is therefore capable of a reliable analysis of denatured, partially degraded proteins and protein fragments. Protein microarrays and peptidomics are combined in a single system capable of simple yet quantitative protein analysis from real samples (i.e. imperfectly stored, partially degraded samples, scene-of-crime applications, etc.).

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