A brief summary of the technique of species identification by interrogation of protein sequence using bottom up proteomics approaches is presented. Instrumentation and software are discussed along with problems of posttranslational, post-mortem and high temperature processing modifications to proteins and amino acids that can affect the subsequent interpretation of protein sequence data from high temperature processed meat and bone meal (MBM). Three approaches are described, using a combination of protein purification techniques and mass spectrometry, which can be used to identify animal protein present in MBM through the sequence analysis of the bone protein collagen or the muscle proteins myosin and troponin I.