Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism’s proteome—even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database—as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a “species-specific” peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.

We studied positive associations among seabirds and marine mammals at South Georgia on research cruises during the Austral winters of 1985, 1991 and 1993 and found statistically significant differences. We collected data on abundance and distribution, providing a critical reference for sub-Antarctic conservation in anticipation of future environmental changes. We found significant changes in the abundance of 29% of species surveyed and a consequent change in species diversity. We postulate that the resulting altered community composition may have previously unanticipated population effects on the component species, due to changes in positive interactions among species which use each other as cues to the presence of prey. We found a near threefold reduction in spatial overlap among vertebrate predators, associated with warming sea temperatures. As the strength and opportunity for positive associations decreases in the future, feeding success may be negatively impacted. In this way, environmental changes may disproportionately impact predator abundances and such changes are likely already underway, as Southern Ocean temperatures have increased substantially since our surveys. Of course the changes we describe are not solely due to changing sea temperature or any other single cause—many factors are important and we do not claim to have removed these from consideration. Rather, we report previously undocumented changes in positive associations among species, and argue these changes may continue into the future, given near-certain continued increases in climate-related changes.

Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.