• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Live Online Course – 1st Edition

Palaeoproteomics and Zooarchaeology by Mass Spectrometry (ZooMS)

November 2nd-9th, 2023

Live sessions will be recorded

Course Palaeoproteomics and Zooarchaeology by Mass Spectrometry (ZooMS)


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Course Overview & Programme

In this course, participants will be introduced to paleoproteomic methods that will include various R packages including MALDIquant, for ZooMS MALDI peptide mass fingerprint-based species identification, MSFragger for sequencing and an introduction to incorporating proteomic sequence data into molecular phylogeny reconstruction using MEGA.

During the course, participants will first be introduced to some theory with illustrative examples (both from simulated data as well as some real datasets) and will then learn how to interpret the data as well as how to assess their reliability.

  • Introduction to ancient proteins and reasons for analysing them and the most appropriate biochemical methods to do so, relating to sample type
    • Short introduction on protein structure, evolution, and ongoing investigations in zooarchaeology and palaeobiology
  • Learn the basics of proteomics
    • Introduction to the differences between ionization techniques, mass analysers, and fragmentation methods.
    • Illustration with worked examples of de novo sequencing peptides and probability-based sequence matching.
  • Identifying a species from a peptide mass fingerprint
    • Introduction on how to identify ancient collagen fingerprints and understand the confidence levels for taxonomic assignment
    • Learn the use of automated tools for identification that include machine learning, and understand their limitations
  • Learn to characterise the proteome of an ancient sample
    • Learn how to interpret sequence data from complex samples of unknown species
    • Identify confidence levels of cross-species sequence interpretations through protein BLAST and the Ensembl Genome Browser
  • Introduction to the basics of molecular phylogenies from protein sequences
    • Learn how to create a molecular phylogeny in MEGA
    • Understand the limitations of partial sequence data derived from ancient samples
  • Summary
    • Summary on the various techniques’ strengths and weaknesses, assumptions for each approach, some of the standard open source tools available, and alternative tools currently available on R with some worked examples.

Graduate or postgraduate degree in Biomedical, Life or Earth Sciences. Familiarity with R is highly recommended.

Participants must have a personal computer (Windows, Mac, Linux). The use of a webcam and headphones is strongly recommended, and a good internet connection.


Dr. Michael Buckley
University of Manchester

Dates & Schedule

November 2nd-9th, 2023

13:00-17:00 (Madrid time zone)

Online live sessions on 2, 3, 6, 8, and 9 November; 13:00 to 17:00 (Madrid time zone), plus 4 hours of participants working on their own.

Total course hours: 24 

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.



This course will be delivered live online

The course will be taught using a combination of live (synchronous) sessions on Zoom and Slack.
Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.


Places are limited to 12 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until September 30th, 2023):
  • 490 €
    (392 € for Ambassador Institutions)
  • Regular (after September 30th, 2023):
  • 676 €
    (540.80 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.