PhD Student

Last application date
Jan 13, 2023 00:00
Department
FW01 - Department of Pharmaceutics
Contract
Limited duration
Degree
Masters in Pharmacy, Masters in Bioengineering, Masters in Biomedical sciences, Masters in Biochemistry, Masters in Molecular Biology or alike
Occupancy rate
100%
Vacancy type
Research staff

Job description

Background: The candidate will help develop and upscale a novel pandemic preparedness diagnostic assay that detects and quantifies viral and host inflammation biomarker peptides using mass spectrometry. This assay was co-developed by the ProGenTomics lab and is therefore still very novel and groundbreaking. It has been proven very efficient for the detection and quantification of Sars-Cov-2. More specifically, it uses Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) technology to enrich and quantify proteotypic peptides of the N protein from trypsin-digested samples from COVID-19 patients. The Cov²MS assay was shown to be compatible with a variety of sample matrices including nasopharyngeal swabs, saliva and blood plasma and shows a strong positive correlation with qPCR detection up to the level where no live virus can be cultured from patients. The automatable “addition only” sample preparation, digestion protocol, peptide enrichment and subsequent reduced dependency upon LC allow analysis of up to 500 samples per day per MS instrument. Importantly, peptide enrichment allowed detection of N protein in a pooled sample containing a single PCR positive sample mixed with 31 PCR negative samples, without loss in sensitivity.
Job Description: The candidate will further develop the assay into a tool enabling longitudinal epidemiological monitoring of large numbers of pathogens within a population, applied as an early warning system (as described in https://doi.org/10.7554/eLife.75471). The work will be done in the framework of a European funded project for Disaster-Resilient Society: “ONELAB: Orchestrating next-generation mobile modular laboratories for pandemic monitoring preparedness”. The candidate will have to combine discovery proteomics on high resolution QTOF instruments (for blood inflammation and novel viral peptide biomarker discovery) with optimization of targeted assays on triple quadrupole designs (both with and without prior SISCAPA peptide enrichment).

Job profile

Wet lab sample preparation (both manual and with liquid handling robotics) and data analysis are considerable portions of the work. ProGenTomics has its own MS core facility and the candidate can spend considerable hands-on time at the different instruments as well.

The candidate should have a (strong) background in mass spectrometry, preferably in proteomics applications. With over 20 other labs involved in the project, the candidate should have good communication skills, including with people that have different expertise. A strong knowledge of the English language is required. The interdisciplinary team of ProGenTomics will also provide a rich context introducing the candidate into forensic and paleoproteomics as well as epigenetic research on histones, all of which can inspire the further development of the pathogen diagnostic assay.

How to apply

Applications can be sent to maarten.dhaenens@ugent.be

  • Motivation letter including how the candidate meets the profile criteria;
  • Academic curriculum vitae (including a list of publications, a list of courses and a list of talks given);
  • Contact details for three references familiar with your academic work.