Proteins from the Past: Palaeoproteomic Methods

Course content

This course 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 in all the laboratory activities defining the most advanced workflow currently used in a standard palaeoproteomic study. Hands-on sessions will start with the preparation of authentic ancient samples for proteomics analysis, continuing with high-resolution tandem MS data production, and concluding with the analysis and 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.

Indicative schedule:

Week 1: Introductory lectures: history of palaeoproteomics and key discoveries

Week 2: Introductory lectures (continued): most advanced applications of palaeoproteomics

Week 3: Sample preparation

Week 4: Sample preparation (continued) and nanoLC-MS/MS

Week 5: Lectures: methods that enabled key palaeoproteomics achievements

Week 6: MS data analysis

Week 7: Palaeoproteomic data interpretation and reporting

Learning outcome

By the end of the course, you will:

  • Clearly identifying the molecular peculiarities distinguishing ancient proteins to better decide which protein extraction strategies you should adopt, and what mistakes you should avoid, maximise protein recovery during sample preparation preparation
  • Recognize 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
  • Analyzing ancient proteome sequences in preparation of their phylogenetic interpretation,
  • Evaluate the robustness and reliability of palaeoproteomics result, either yours or previously published.

Lectures, exercises, laboratory activities, group work and essay writing.

Literature will be given 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.

The students are strongly recommended to bring their own PC laptop for the data analysis activities.

Continuous feedback during the course of the semester
Feedback by final exam (In addition to the grade)
7,5 ECTS
Type of assessment
Written assignment
Type of assessment details
The students will have to process, interpret and present the results obtained from the analysis of the experimental data they generated during the course, in a peer-reviewed article format including the following sections:
- Introduction
- Materials and methods
- Results and Discussions
- Conclusion

Format: individual report will have to be:
- 5-10 pages in length plus references
- written in English and
- submitted within 15 days after the end of the course as a take home assignment
Exam registration requirements

To be admitted to the exam, students must have attended at least 80% of the classes. Exceptions may be made if absence was due to force majeure.

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

If the requirements are 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 assessment

See learning outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 25
  • Preparation
  • 38
  • Laboratory
  • 35
  • Exam Preparation
  • 63
  • Exam
  • 45
  • English
  • 206


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 3
Study Board for the Biological Area
Contracting department
  • Globe
Contracting faculty
  • Faculty of Health and Medical Sciences
Course Coordinators
  • Enrico Cappellini   (11-6e6c6a79796e7575727772497c7e776d37747e376d74)
  • Alberto John Taurozzi   (16-6f7a707380827d3c826f83807d8888774e81837c723c79833c7279)
Saved on the 27-02-2024

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