Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In archaeological or paleontological field, PMF is known as ZooMS and is widely implement-ed to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to ten-fold the required bone sample amount (down to milligram scale) and achieves robust deamidation value calculation in a high throughput manner. These improvements rely on a 96-well plates samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious posttranslational modifi-cations production and peptide mass fingerprinting at high resolution using MALDI-FTICR (Matrix Assisted Desorption Ionization Fourier Transform Ion Cyclotron Resonance) analysis. This method was applied to the identification of a hun-dred bones of herbivores from the Middle Paleolithic site of Caours (Somme, Northern France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their oste-omorphology, as well as to more challenging bone samples consisting of small or burnt bone fragments. The obtained de-amidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.