Protein-based human identification (PBHI) is a novel and innovative tool that has potential to be used by forensic investigators within Australia to associate evidence with a suspect. DNA-based human identification is more familiar, but both methods are complementary and take advantage of an individual’s biological variation. Proteomic genotyping of the human hair shaft detects genetically variant peptides (GVPs) that result from single amino acid polymorphisms. These GVPs can be used to complement established DNA-based methods or be used when these methods fail to provide a forensically useful answer. A core focus will be the development of this technology to the point where they can be used to infer the profile of matching genetic variation and to use this in a legal context. Firstly, mirroring established methodology, an investigation of the feasibility to perform human hair shaft proteomic genotyping within a forensic toxicology setting was conducted. Extractions of genetically variant peptides (GVPs) from human hair shaft test samples were performed prior to analysis on a QE Plus Orbitrap instrument equipped with ultra-high performance liquid chromatography, a typical forensic toxicology platform. Data analysis was performed using Proteome Discover and evaluated against published results for test samples under investigation. The combined total of GVPs identified from the test extracts was 80. Comparing the data to a pre-established GVP panel consisting on 24 (12 variants), 11/12 GVPs were identified in multiple test samples. Additional GVP variants were also identified. Verification of two test extracts GVPs to published data; 11/11 and 14/15 GVPs were identified correctly. These results are promising and indicate huge potential of this information for human identification and forensic intelligence. The approach detailed here exploits new advances in protein science and forensic toxicology.