PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology

ZooMS (Zooarcheology by Mass Spectrometry) is a rapid and cost-effective method for species identification of animal remains through peptide mass fingerprinting. After mass spectrum generation, a common way to perform taxonomic identification is to compare the mass fingerprints to a reference database of diagnostic peptide markers to determine the species of origin. This analytical stage, however, is tedious and error-prone, often necessitating a manual examination of spectra. In this article, we present a comprehensive approach to automate and standardize the usage of peptide markers and the classification of ZooMS spectra. We have developed software called PAMPA (protein analysis by mass spectrometry for ancient species), for which we demonstrate the effectiveness using a variety of spectral data from bone samples generated by MALDI-TOF and MALDI-FTICR. PAMPA is open source and comes with a database of peptide markers and a collection of curated COL1A1 and COL1A2 sequences. We believe it will be a valuable resource for the scientific community.