title: Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone.
abstract: BACKGROUND
  We report the use of proteomics techniques to study how the fossil bone proteome changes in complexity over one million years.
  
  
  METHODS
  We include the attempted use of a previously unreported methodology in proteome research, to remove the dominant bone collagens using bacterial collagenase as well as conventional shotgun proteomics methodology following digestion with the protease trypsin. In this study we expand upon a set of 19 bovine sub-fossil specimens ranging over one and a half million years that had previously been shown to possess collagen, using a total of 46 LTQ-Orbitrap liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses containing 462,186 precursor ion analyses.
  
  
  RESULTS
  Although many types of proteins can typically be identified in recent bone, in degraded bone we observe a rapid loss of lower abundance proteins. Abundant serum proteins such as serum albumin and alpha-2-HS-glycoprotein appear to be more easily recovered in ancient bone, both being identified in specimens dating to the Early Pleistocene, the earliest period tested in this study. Proteins belonging to the leucine-rich repeat family such as lumican, biglycan and chondroadherin also survive well, possibly because of their interactions with bone collagen.
  
  
  CONCLUSIONS
  Of these 'survivor proteins' A2HSG shows a remarkable amount of sequence variation, making it potentially one of the most useful proteins to study for species identification and phylogenetic inference in archaeological and palaeontological bone.
authors: Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
authors: Caroline
authors: C
authors: Wadsworth
authors: Mike
authors: M
authors: Buckley
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001842:Bone and Bones / Q000737:chemistry*; D002417:Cattle; D017364:Collagenases; D005580:Fossils; D006115:Greece; D019791:Guanidine; D008969:Molecular Sequence Data; D060066:Protein Interaction Maps; D011506:Proteins / Q000032:analysis* / Q000737:chemistry / Q000145:classification; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D006113:United Kingdom
chemical_list: D011506:Proteins; D020543:Proteome; D017364:Collagenases; D019791:Guanidine