Digested protein extracts were analysed independently by ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) using a workflow described previously [34 (link)]. Separation was performed on an Ultimate 3000-RSLC system (Thermo Fisher Scientific) with a RSLC Polar Advantage II Acclaim column (2.1 × 100 mm, 120 Å, 2.2 µm) using a flow rate of 300 µl min–1 and mobile phase gradient of A: H2O + formic acid (FA) 0.1% and B: acetonitrile + FA 0.08%. We used a high-resolution ESI-Q-TOF mass spectrometer (Maxis II ETD, Bruker Daltonics) in positive mode and data-dependent auto-MS/MS mode on the m/z range 200–2200. MS/MS spectra were generated using collision-induced dissociation by selection of ions with charge states between 2+ and 5+ and on m/z range 300–2200. Calibration was carried out for each run with sodium formate clusters and experimental blanks analysed every five samples for each of the runs with modern references and archaeological samples.
Le Meillour L., Zazzo A., Zirah S., Tombret O., Barriel V., Arthur K.W., Arthur J.W., Cauliez J., Chaix L., Curtis M.C., Gifford-Gonzalez D., Gunn I., Gutherz X., Hildebrand E., Khalidi L., Millet M., Mitchell P., Studer J., Vila E., Welker F., Pleurdeau D, & Lesur J. (2023). The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa. Royal Society Open Science, 10(11), 231002.
Other organizations :
Centre National de la Recherche Scientifique, Molécules de Communication et Adaptation des Micro-organismes, University of Copenhagen, Archéozoologie et Archéobotanique, Histoire Naturelle de l’Homme Préhistorique, Sorbonne Université, University of South Florida St. Petersburg, Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés, Natural History Museum of Geneva, California State University, Channel Islands, University of California, Santa Cruz, Museum of London Archaeology, University of Cambridge, Ministère de la Culture, Université de Montpellier, Institut National de Recherches Archéologiques Préventives, Stony Brook University, Université Côte d'Azur, Cultures et Environnements. Préhistoire, Antiquité, Moyen Âge, Louvre, Université Claude Bernard Lyon 1, Archéorient
UHPLC-MS/MS workflow and parameters, including column, flow rate, mobile phase gradient, and mass spectrometer settings
Calibration of mass spectrometer with sodium formate clusters
Analysis of experimental blanks every five samples
controls
Positive control: Modern reference samples
Negative control: Archaeological samples
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