Timothy P Cleland1, Julianne J Sarancha2,3, Christine A M France1. 1. Museum Conservation Institute, Smithsonian Institution, Suitland, MD, 20746, USA. 2. School Of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA. 3. School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
Abstract
RATIONALE: Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed. METHODS: Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by LC/MS using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed with MetaMorpheus and custom R scripts. RESULTS: We found a variety of proteins in addition to collagen, although collagen I was the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages allowing their use in single amino acid stable isotope analyses. CONCLUSIONS: All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses. This article is protected by copyright. All rights reserved.
RATIONALE: Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed. METHODS: Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by LC/MS using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed with MetaMorpheus and custom R scripts. RESULTS: We found a variety of proteins in addition to collagen, although collagen I was the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages allowing their use in single amino acid stable isotope analyses. CONCLUSIONS: All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses. This article is protected by copyright. All rights reserved.