Practical Palaeoproteomics Summer School

Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.

Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

Learning objectives
A student who has met the objectives of the course will be able to:
1. Extract protein residues from small quantities of precious or unique fossil, archaeological, forensic, or artistic specimens preventing contamination.
2. Use proteomics software (i.e. MaxQuant and PEAKS) for basic, and in some cases advanced, data exploration and analysis.
3. Authenticate the proteins retrieved from ancient samples and evaluate the chemical damage affecting them.
4. Identify the research challenges in palaeontology, paleoanthropology, archaeology, forensic and cultural heritage studies that palaeoproteomics can successfully address.
5. Understand major decay mechanisms, and therefore better appreciate how extraction protocols are optimised for ancient proteins.

Content
This intensive eight-day summer course will provide the attendees 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 forensic medicine, and cultural heritage conservation will also be described.

The students will actively take part in laboratory and data analysis activities covering the entire standard palaeoproteomic workflow. Hands-on sessions (5 days, 7-8 hours each day) will start with preparation of ancient bone or tooth samples for proteomics analysis, continuing with high-resolution tandem MS data generation (attendees will not operate the LC-MS/MS instrument), and concluding with the analysis and the interpretation of the data the students generated themselves.

A series of introductory lectures, that can be attended remotely or in-person (3 days, 6.5 hours each day), will present:
(i) the history of this research field,
(ii) the most advanced technologies and methodologies it relies on, and
(iii) the most relevant scientific achievements it accomplished.

Indicative programme
1. 14th August: History of Palaeoproteomics and Key Discoveries – Online or in-person attendance
2. 15th August: Applications I (Cultural Heritage) – Online or in-person attendance
3. 16th August: Applications II (Forensics and Evolution) – Online or in-person attendance
4. 19th August: Sample Preparation – Hands-on, in-person attendance
5. 20th August – Sample Preparation (continued) – Hands-on, in-person attendance
6. 21st August – MS data analysis Lectures and Tutorials – Hands-on, in-person attendance
7. 22nd August – Supervised Basic Data Analysis – Hands-on, in-person attendance
8. 23rd August – Basic Data Analysis and Advanced Concepts – Hands-on, in-person attendance

Participants
The target group for this course are PhD fellows that wish to integrate proteomic analysis in their research activities. The course will be of special interest to those focusing on paleontology, paleoanthropology, archaeology, forensic medicine, or cultural heritage studies.

Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:
• Life, Earth and Environmental Sciences
• Oral Sciences, Forensic Medicine and Bioanthropology
• Immunology and Infectious Diseases

Language
English

Form
Lectures, practical laboratory training, practical data analysis training and exercises.

Course directors
Enrico Cappellini: Associate Professor, Globe Institute, University of Copenhagen, ecappellini@sund.ku.dk
Alberto Taurozzi: Assistant Professor, Globe Institute, University of Copenhagen, alberto.taurozzi@sund.ku.dk

Teachers
Enrico Cappellini: Associate Professor, Globe Institute, University of Copenhagen
Alberto Taurozzi: Assistant Professor, Globe Institute, University of Copenhagen
Jesper V. Olsen: Professor, NNF Center for Protein research, University of Copenhagen
Matthew Collins: Professor, Globe Institute, University of Copenhagen
Frido Welker: Associate Professor, Globe Institute, University of Copenhagen
External invited speakers

Dates
14th-23rd of August 2024

Course location
Kommunehospitalet: Øster Farimagsgade 5, 1353 København
Note: the first three days of the course (14th-16th of August) can also be attended online remotely

Registration
Please register before 1st of June 2024

Expected frequency
Once a year in August (block 5)

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.