SGBK20012U Proteins from the Past: Palaeoproteomic Methods

Volume 2021/2022

This intensive seven-days summer course (7-8 hours each day) will provide you with a detailed introduction to the methods used for mass spectrometry (MS)-based ancient protein sequencing, i.e. palaeoproteomics. The course will focus on the most advanced methodologies and applications of palaeoproteomics to palaeontology, palaeoprimatology and palaeoanthropology. Applications of palaeoproteomics to cultural heritage (CH) studies and conservation will also be described.
The students will actively take part to all the laboratory activities defining the most advanced workflow currently used in a standard palaeoproteomic study. Hands-on sessions will start with preparation of authentic ancient samples for proteomics analysis, continuing with high-resolution tandem MS data production, and concluding with the analysis and the interpretation of the data the students generated themselves.
A series of lectures will present: (i) the history of this research field, (ii) the most advanced technologies and methodologies it relies on, and (iii) the most impressive scientific achievements it accomplished.

  1. Indicative schedule:
  2. Day 1: Introductory lectures: history of palaeoproteomics and jey discoveries
  3. Day 2: Introductory lectures (continued): most advanced applications of palaeoproteomics
  4. Day 3: Sample preparation
  5. Day 4: Sample preparation (continued) and nanoLC-MS/MS
  6. Day 5: Lectures: methods that enabled key palaeoproteomics achievements
  7. Day 6: MS data analysis
  8. Day 7: Palaeoproteomic data interpretation and reporting
Learning Outcome

By the end of the course, you will:

  • Clearly identify the molecular peculiarities distinguishing ancient proteins to better decide which protein extraction strategies you should adopt, and what mistakes you should avoid, to maximise protein recovery during sample preparation
  • Recognise and exclude possible contaminants in your samples
  • Identify 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 an ancient biological or CH specimen preventing contamination and dealing with very small quantities of precious and unique starting material,
  • Confidently and autonomously use the most common software, i.e. MaxQuant and PEAKS, for basic, and in some cases advanced, peptide-spectrum matching,
  • Characterise and quantify the molecular damage affecting ancient proteins in an ancient specimen,
  • Discover amino acid substitutions exclusively present in extinct organisms;


  • 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.

Literature will be provided prior to the start of the course alongside the course compendium.

Applicants should have a bachelor degree in archaeology, biology, chemistry, biochemistry, geology or a related field.
Lectures, exercises, laboratory activities and group work.
  • Category
  • Hours
  • Lectures
  • 20
  • Preparation
  • 29,5
  • Laboratory
  • 34
  • Exam Preparation
  • 36
  • Exam
  • 18
  • Total
  • 137,5
Continuous feedback during the course of the semester
Feedback by final exam (In addition to the grade)
Type of assessment
Written assignment
On the last day of the course, students will be given the title of a set essay, of 5-6 pages in length, to be written in English and to be submitted within 7 days as a take home assignment.
Exam registration requirements

Admission to the exam is subject to actively attending the entire one week-long hands-on laboratory activities and the lectures. 

All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners.

If the requirements is not fulfilled the student must hand in a 5-page essay on a relevant topic given by the course responsible before the student can do the re-exam


Criteria for exam assesment

See learning outcome.