SGBK20001U Ancient Proteins and Evolution

Volume 2024/2025

This course will describe how palaeoproteomics (i.e. mass spectrometry-based ancient protein sequencing) can be used to address evolutionary, biological and archaeological questions. There is a growing interest in palaeoproteomics which is building upon the successes of ancient DNA studies. Proteins tend to be more robust than DNA and therefore they can be used to extend research to older (~ 4 million years) samples and hotter (tropical) sites. Thgrough the application of the most advanced palaeoproteomic methods, proteins are now amenable to sequencing even when they represent only a minimal fraction of highly mineralized tissues such as dental enamel. Some of the results obtained using ancient protein analysis are contributing to address general interest challenges in Pleistocene mammalian, including human, evolution. Furthermore, the significance of the pust translational modifications (and therefore the proteomic strategies) investigated in palaeoproteomics is also relevant to studies of ageing, pharmaceutical preparation and food storage/processing.

The course will present and critically comment upon the most recent achievements deriving from the application of palaeoproteomics to palaeontology, paleoanthropology, archaeology and cultural heritage studies. With good amino acid sequence coverage and careful interpretation ancient protein remains can be used to answer fundamental questions of biological evolution.  Proteinaceous materials have also been used as glues, food, paint binders and for clothing. Palaeoproteomics can accordingly be used to explore how humans exploited animals and plant tissues in the past.

At the beginning of the course, a series of lectures will explore the process of protein decay and methodologies from chiral amino acid analysis to tandem mass spectrometry which are being used to recover and authenticate ancient proteins. This will be followed by examples of application of palaeoproteomics to different disciplines.  In a second phase, the students will directly apply the techniques at the base of palaeoproteomic analysis during a 3-week practical activity in a molecular biology laboratory.

Learning Outcome


By the end of the course, you will be able to:

  • Clearly identify the research challenges in palaeontology, paleoanthropology, archaeology and cultural heritage studies that palaeoproteomics can successfully address,
  • Understand major decay mechanisms, and therefore better appreciate how extraction protocols are optimised for ancient proteins,
  • Authenticate the proteins retrieved from ancient samples and to evaluate the chemical damage affecting them.


By the end of the course, you will be able to:

  • Extract protein residues from small quantities of precious or unique fossil, archaeological or artistic specimen preventing contamination,
  • Use proteomics software (i.e. MaxQuant and PEAKS) for basic, and in some cases advanced, data exploration and analysis,
  • Characterise and quantify the molecular damage affecting proteins in ancient specimens,
  • Discover amino acid substitutions exclusively present in extinct organisms as well as chemical modifications caused by diagenesis.


By the end of the course, you will be able to:

  • Judge, and eventually criticise, the content of scientific literature describing palaeoproteomics-based research 
  • Select the most sound approach to process high-throughput tandem MS-based palaeoproteomics data sets
  • Analyse ancient proteome sequences in preparation of their phylogenetic interpretation, 
  • Evaluate the robustness and reliability of palaeoproteomics result, either yours or previously published.

Relevant literature will be provided through Absalon.


Lectures, interactive discussion groups and a 3-week wet-lab practical.
  • Category
  • Hours
  • Lectures
  • 24
  • Preparation
  • 91
  • Laboratory
  • 42
  • Project work
  • 24
  • Study Groups
  • 24
  • Exam
  • 1
  • Total
  • 206
Feedback by final exam (In addition to the grade)
7,5 ECTS
Type of assessment
Oral examination, 20 min under invigilation
Written assignment, 72 hour (take home assignment)
Type of assessment details
Students will be assessed based on one short written take-home assignment and one 20-minute final oral exam. Students will have 20 mins preparation time for the oral exam. The grade is based on an overall assessment.
Exam registration requirements

To be admitted to the exam students must have delivered all of the course assignments and they must have attended at least 80% of the classes.

Only certain aids allowed

Students are only allowed to use materials handed out by the examiners during the 20 min preparation for the oral examination

Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners
Criteria for exam assesment

In order to obtain the grade 12, the student should convincingly and accurately demonstrate the knowledge, skills and competences described under Learning Outcome.