Using state-of-the-art technology, the archaeological science labs of the Max Planck Institute for Evolutionary Anthropology are an essential component in helping to answer key questions in palaeoanthropology. The Archaeological Science group in the Department of Human Evolution has at its fingertips a variety of methods which can provide crucial data on chronology, palaeodiet, migration and phylogenetics. In a first step the team managed to extract and sequence a bone protein, osteocalcin, from two 75,000-year-old Neanderthal specimens from Shanidar in Iraq, which failed to yield DNA. The protein sequencing was achieved using MALDI-TOF/TOF mass spectrometry, a technique which provides exceptional limits of detection. These are the oldest known proteins to be sequenced and have provided new phylogenetic and phenotypic data on the hominid line alongside osteocalcin sequences extracted from related, extant species (chimpanzee, orangutan, gorilla and human). These data illustrate the potential for proteins to provide informative genetic data in the absence of recoverable DNA, and opens up the exciting possibility of applying these techniques to earlier hominids.