SGBK20012U Proteins from the Past: Palaeoproteomic Methods
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
Knowledge:
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,
Skills:
- 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;
Competencies:
- 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.
Literature will be given prior to the start of the course alongside the course compendium.
- Category
- Hours
- Lectures
- 25
- Preparation
- 38
- Laboratory
- 35
- Exam Preparation
- 63
- Exam
- 45
- Total
- 206
Ordinary Registration Period:
November 15th – December 1st 2023.
Late Registration Period:
January 18th – 31st 2024.
Self Service at KUnet
Open for credit transfer students and other external students. Apply here:
Credit transfer students apply here
Other external students apply here
- Credit
- 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.
- Aid
- All aids allowed
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
Several internal examiners.
- Re-exam
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 assesment
See learning outcome.
Course information
- Language
- English
- Course code
- SGBK20012U
- Credit
- 7,5 ECTS
- Level
- Full Degree Master
- Duration
- 1 block
- Placement
- Block 3
- Schedule
- A
- Course capacity
- 20
Study board
- Study Board for the Biological Area
Contracting department
- Globe
Contracting faculty
- Faculty of Health and Medical Sciences
Course Coordinators
- Enrico Cappellini (ecappellini@sund.ku.dk)
- Alberto John Taurozzi (alberto.taurozzi@sund.ku.dk)