Proteomic genotyping uses genetically variant peptides that contain single amino acid polymorphisms to infer the genotype of corresponding non-synonymous SNP alleles. We have focused on hair proteins as a source of protein-based genetic information in a forensic context. An optimized sample processing protocol for hair shafts has been developed for use on a single hair that allows us to conduct validation protocols on real world samples. This includes whether the inferred SNP genotypes are robust and not systematically affected by biological or chemical variation in hair proteomes that might be obtained from a crime scene. To this end we analyzed the hair of 4 mature individuals with a mixture of pigmented and non-pigmented hair. We demonstrate significant changes in the proteomes of grey versus pigmented hair. Vesicle specific proteins and lipid catabolism proteins were enriched in pigmented hair, and housekeeping proteins and lipid anabolic enzymes were enriched in grey, non-pigmented hair. The resulting profiles of genetically variant peptides, however, were more correlated with profiles from the same individuals regardless of pigmentation status. Together with other published evidence, this finding indicates that profiles of genetically variant peptides are robust and more correlated with other genetically variant peptide profiles from the same individual irrespective of changes occurring in the hair protein profile. Based on this small sample, investigators using profiles of genetically variant peptides to infer random match probabilities should not expect to observe differences based on the pigmentation of the hair shaft.