Enhancing ZooMS applications with MALDI-FTICR mass spectrometry on Pleistocene material showing variable collagen preservation

Advances in high-throughput molecular analyses of collagen peptides, especially ZooMS (Zooarchaeology by Mass Spectrometry), have addressed the issue of intense skeletal fragmentation at Palaeolithic archaeological sites, which hinders morphological identification. However, the challenge of variable collagen preservation persists. We aim to evaluate the potential of two mass analyzers TOF vs FTICR to propose novel options to enhance the ZooMS workflow. Type 1 collagen (COL1) was extracted from 89 archaeological bones from the site of Le Piage (France, 37-34 ka cal BP). Three distinct ZooMS protocols were used: an acid-free method (AmBic) and two demineralizations (HCl and TFA), combined with MALDI-TOF and MALDI-FTICR instruments. The first offers rapid and cheap analysis, while the second provides higher resolution. Taxonomic identifications were made by peptide mass fingerprinting (PMF). Finally, LC-MS/MS was applied to verify 26 low-collagen samples identifications.