Two PhD positions in Mass Spectrometry-based Palaeoproteomics

Updated: 4 months ago
Deadline: 15 May 2017

Two PhD positions in Mass Spectrometry-based Palaeoproteomics
Marie Curie TEMPERA European Training Network

Two PhD positions that are part of the Marie Skłodowska-Curie TEMPERA European Training Network (www.tempera-etn.eu ) are available in the group of Jesper Olsen at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic protein research and comprises a wide range of expertise and technology platforms including mass spectrometry, imaging, protein production and biophysical characterization. The “Mass Spectrometry for Quantitative Proteomics” group is headed by Prof. Dr. Jesper V. Olsen, who is also vice director of the Center. Associate Prof. Christian Dahl Kelstrup is the deputy of the group and he will supervise one of the PhD students. The goal of the Olsen group is to develop and apply mass spectrometry-based proteomics technologies to solve questions in biology and biomedicine. The two PhD positions are part of the Marie Skłodowska-Curie TEMPERA European Training Network (ETN) supported by the European Union's EU Framework Programme for Research and Innovation Horizon 2020 (grant agreement number 722606), www.tempera-etn.eu .


Background

TEMPERA ETN aims at providing international and interdisciplinary state-of-the-art doctoral training to prepare the next generation of specialists in mass spectrometry (MS)-based ancient protein residues analysis for biomolecular diagnostics and conservation of cultural heritage material. Europe’s cultural heritage plays a fundamental role in European cultural integration and attracts millions of visitors each year. Most of the cultural heritage objects produced using biogenic materials are rich in protein residues. Proteomic analysis of cultural heritage will improve knowledge about production techniques and chemical preservation of cultural heritage materials, ultimately improving their safeguard and conservation. For the first time, TEMPERA brings together in a network the laboratories which have, largely in isolation, developed the techniques upon which ancient protein analysis is built. Ancient proteomics is a relatively new research field that is really taking off at the moment, and our group has over the last five years worked closely with the Natural History Museum of Denmark to analyze proteins from ancient material. We have used orbitrap technology to analyze tens of thousands of years old proteomes from Mastodon (Waters et al, Science 2011: PMID: 22021854); Mammoth (Cappellini et al, J. Proteome Res. 2012: PMID: 22103443), a prehistoric horse (Orlando et al, Nature 2013: PMID: 23803765), teeth from old human skeletons (Warinner et al, Nature Genetics 2014: PMID: 24562188); and South American ungulates (Welker et al, Nature 2015: PMID: 25799987). For these two PhD positions we are looking for PhD candidates with interest in ancient proteomics and expertise in mass spectrometry.

For more information about the research group please visit: http://www.cpr.ku.dk/olsen/

If you still have questions, contact us: jobs@cpr.ku.dk


Project Descriptions

General: The PhD research projects aims at developing and applying tandem mass spectrometry (MS/MS) based methods and associated computational proteomics strategies to analyze the composition of proteinaceous paint binders in sculpted materials and architectural decorations to improve our understanding and perception of the original appearance of painted objects. The project will also require careful development of activities for public engagement as well as writing scientific articles, papers, reports or books, as appropriate. The selected PhD candidates will also be required to attend network-wide workshop events and take active part to network-wide remote activities. The candidates should be able to conduct independent and creative research, demonstrate scientific productivity, and show good inter­personal and communication skills.

The following two Early Stage Researcher (ESR) positions are available:

ESR6: Development of Top-down palaeoproteomics (@ UCPH, supervisor Jesper V. Olsen).

The candidate will work in close collaboration with ESR8 on optimizing and improving the MS/MS capabilities of orbitrap tandem mass spectrometers for ancient protein sequencing to confidently identify the biological species of origin and the raw materials used as binders for the polychrome decoration of ancient sculptures and architecture. The project aims to develop alternative and complementary strategies to traditional shotgun proteomics of ancient proteins, which typically relies on tryptic digest of the proteins prior to MS analysis.

The candidate will explore nano-scale liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) for ancient protein analysis with and without a digestion step using different ion dissociation methods.

Tandem mass spectrometry of ancient proteins and peptides based Electron transfer dissociation (ETD) and ultra-violet photo-dissociation (UVPD) will be benchmarked against the conventional collisional-activation based methods, low-energy collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), as well as hybrid fragmentation methods such as the combination of electron-transfer and higher-energy collision dissociation (termed EThcD). The complementarity of the different types of fragmentation methods is expected to significantly increase confidence in peptide and protein identification in particular for PTM analyses. Development and application of such methods to study proteomes of cultural heritage materials will remove many of the limits hampering analysis of this category of samples.

ESR8: Mass Spectrometry Hardware for palaeoproteomics (@ UCPH, supervisor Christian Dahl Kelstrup).

The candidate will work in close collaboration with ESR6 and take advantage of the recently introduced Orbitrap Fusion Lumos Tribrid mass spectrometer, which is the industry-leading high-performance mass spectrometer equipped with the higher capacity ETD HD fragmentation mode and benefitting from improved transmission of ions into the Orbitrap analyzer. The candidate will utilize this for top-down sequencing of ancient protein analytes present in very small amounts. The main advantages of the top-down approach include the ability to detect degradation products, sequence variants, and combinations of post-translational modifications. Aiming at minimizing preparation steps to maximize recoveries of analytes from cultural heritage objects, ESR8 will develop MS procedures to apply top-down tandem MS protein sequencing to undigested protein extracts of cultural heritage samples, by taking full advantage of the Orbitrap Fusion Lumos Tribrid advanced features. This instrumentation is available at both University of Copenhagen and Thermo Fisher Scientific in Bremen.

Projected start date: September 1st , 2017.

Qualifications

The candidate is required to have a master of science or equivalent degree in biotechnology, natural or medical sciences. Prior knowledge and skills in mass spectrometry and proteomics is a requirement.

The candidates are expected to have experience in:

  • Analytical chemistry, basic biochemistry procedures and basic statistics.
  • Prior knowledge in computational proteomics is considered a distinct advantage.
  • Prior experience with orbitrap based high performance mass spectrometry is not essential, but would be considered an advantage.
  • Good communication skills in English, both oral and written.
  • Strong scientific track record, including research publications in peer reviewed international journal is a plus.
  • Analytical skills and talent for devising innovative scientific or technical solutions.
  • Demonstrate enthusiasm, motivation, flexibility and confidence.

Eligibility

TEMPERA is a Marie Skłodowska-Curie European Training Network. PhD candidates within the TEMPERA ETN program are expected to fulfil the conditions for international mobility. Namely,at the time of recruitment by the University of Copenhagen, researchers must not have resided or carried out their main activity (work, studies, etc.) in Denmark for more than 12 months in the 3 years immediately prior to their recruitment. Short stays, such as holidays, are not taken into account. The applicant must also fulfil the criteria of an Early Stage Researcher. Specifically, at time of recruitment the researcher must be in the first 4 years (full-time equivalent research experience) of his/her research career and must not have been awarded a doctoral degree.

Place of employment and work, secondment

The employment is at Novo Nordisk Foundation Center for Protein Research (www.cpr.ku.dk ) and the successful applicants will mainly be based at the Proteomics Program at the Center, part of the Faculty of Health and Medical Sciences at University of Copenhagen, in Copenhagen city center. The research environment at CPR is vibrant, ambitious, and international, with approx. 30 different nationalities currently represented. The Center comprises modern laboratories and state-of-the-art facilities within protein science. Seminars with high­profiled international speakers and regular internal research seminars are organized at CPR. Secondments at other institutions within the TEMPERA consortium are a mandatory part of the successful researcher’s employment. Accordingly, the selected PhD candidate is expected to spend time, for no more than 11 months, studying and performing interdisciplinary research at different TEMPERA institutions.

Terms of salary and employment

The terms of appointment (including salary and pension) are attractive and will be in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State and according to the rules and regulations laid down by European Union’s rules regarding Horizon 2020 Marie Sklodowska-Curie Initial Training Networks.

Duration: 3 years

Application

Your application should be submitted electronically via the APPLY NOW button below. 

Your application should include the following documents:

  • Motivated letter of application
  • Curriculum vitae, incl. education and experience
  • List of publications, awards and grants
  • Letters of recommendation
  • Names and contact details for two referees

Deadline for application: 15 May 2017

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself. You can read about the recruitment process at www.employment.ku.dk

For further information about the position or the process or if you experience any technical difficulty with the online submission system, please contact CPR: jobs@cpr.ku.dk

CPR and the University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background.


Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.


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