Most routine palaeoproteomic analysis falls under the category of shotgun proteomics, a high-resolution method to analyse archaeological and palaeontological materials which utilises a tandem mass spectrometer. This method is suited to projects that seek to identify the entire proteome present within a sample, those proteins that may be present in low abundances, and samples that have a complex mixture of potential proteins present. While the protein component of bone, for example, may be dominated by type-I collagen, there is a host of proteins present within these archaeological tissues that may be more informative than collagen alone. Enamel is another excellent candidate for shotgun proteomics, as proteins are present in low abundance but can be highly informative and are crucial to evolutionary studies. 

ZooMS (Zooarchaeology by Mass Spectrometry) or peptide mass fingerprinting is an alternative form of palaeoproteomic analysis, which is principally used as a form of taxonomic identification. Rather than attempting to capture the entire proteome, ZooMS targets a single dominant protein, like type-I collagen in bone. The method is predominantly applied to collagenous artefacts like bone, leather, dentine, and ivory, which have the most robust established reference libraries. Additional and smaller reference libraries exist for eggshell and keratinaceous samples, like feathers and horn. The method is highly time and cost-efficient in comparison with other biomolecular processes, allowing for the analysis of large numbers of samples within a short time period.