This study evaluated the application of label-free, relative quantification of highly processed meat proteins to authenticate processed meat products. Quantitation was based on proteins for which heat-stable and species-specific peptide markers had been detected. Using nano-LC-QTOF-MS/MS, 20 new, heat-stable peptide markers unique to chicken, duck and goose were identified, with significant scores. The method enabled detection of 1% (w/w) of chicken and 1% (w/w) pork in a mixture of the meat of three species, as well as 0.8% (w/w) beef proteins in commercial poultry frankfurters. The proteins’ abundance was computed using a spectral matching technique, termed the absolute protein expression (APEX) proteomics tool. This method includes a correction factor for each protein, based on the peptide MS detection probabilities, which are influenced by the physicochemical properties of the peptide. Considerable differences in abundance of myofibrillar and sarcoplasmic proteins were observed between samples and illegal proportions of ingredients were discovered.