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as a Doctoral Candidate (DC)

MobiliTraIN is looking for 13 talented and motivated Doctoral Candidates (DCs) to join us on the journey towards unveiling the potential of IM-HRMS as a key technology for safer therapeutics, better understanding of complex disease progression and improved monitoring of food, water and public health safety.

What MobiliTraIN offers

A thorough scientific education in the frame of a doctoral training programme.
The possibility to participate in specific international courses, workshops and conferences.
A strong involvement in a European research project with high international visibility.
The possibility to perform research visits to internationally renowned research labs in Europe.
A prestigious three-year MSCA Fellowship.
A competitive salary, including mobility and family allowances.

Eligibility criteria

Specific Eligibility Criteria of the Horizon Europe Marie Skłodowska-Curie (MSCA) programme apply, including the mobility rule and PhD rule. Applicants of any nationality are welcome to apply.

Mobility rule: Researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of the host organisation for more than 12 months in the 3 years immediately before the recruitment date (i.e., the start of employment).
PhD Rule: Applicants must be doctoral candidates, i.e., not already in possession of a doctoral degree at the date of the recruitment.
Additionally, PhD applicants must fulfil the local requirements of the recruiting institutions, which are listed in the project descriptions.

Positions

Apply to one of our open positions below. For more details about the positions and the application process, please refer to the links in the individual descriptions.

DC1: Prediction of Collision Cross Sections for De Novo Identifications

Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy

Berlin, Germany

Supervisor: Prof. Dr. Kevin Pagel

The aim of this particular project is the development and refinement of models for the theoretical prediction of collision cross sections. Central for this will be the in-depth structural characterisation of few selected standards using a combination of gas phase infrared spectroscopy, ion mobility spectrometry and density functional theory. This includes:

Recording multidimensional datasets consisting of m/z, CCS, and high-resolution gas phase IR spectra for ten selected biomolecular standards.
Development of a trajectory-method based algorithm for de novo CCS prediction.
Evaluation of the potential for IM-HRMS-based structural identification of compounds.

Application deadline: To receive full consideration, applications must be submitted before 11 March 2024.

DC2: Ion mobility of oligonucleotide and peptide-based therapeutics

University of Geneva, Bioanalytical Mass Spectrometry, School of Pharmaceutical Sciences

Geneva, Switzerland

Supervisor: Prof. Dr. Valérie Gabelica

1) Delineate which solution conditions (solvents, additives) produce the most robust and predictable charge states and ion mobility collision cross section distributions; 2) Test how ion internal energy affects the gas-phase structural ensembles and thus the interpretation of the ion mobility results; 3) Understand which chemical classes of molecules (size, type of interactions involved) are susceptible to unwanted collision-induced conformational changes before ion mobility analysis; 4) Evaluate the utility of IM-HRMS for oligonucleotide and folded peptide analysis in the pharmaceutical industry.

Application deadline: To receive full consideration, applications must be submitted before 23 May 2024.

DC3: Characterising and controlling internal energy in trapped ion mobility spectrometry, and its impact on structural chemistry, structural biology, and multi-omics

Bruker Daltonics GmbH & Co. KG (BRUKER)

Bremen, Germany

Supervisor: Dr. Eduardo Carrascosa

1) Locate, quantify and control the effect of the ion’s translational temperature on their internal temperatures and potential fragmentation in different TIMS configurations. 2) Develop and demonstrate a 1^st order CCS determination. From the TIMS theory, this technique will be comparable to the well-established 1^st order CCS determination on the drift tube IMS instruments.

DC4: IM-HRMS for improved therapeutic monoclonal antibody-based formats characterisation

Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien – IPHC UMR

Strasbourg, France

Supervisor: Dr. Sarah Cianferani

1) Develop new intact and middle-level analytical methods based on the combination of non-denaturing LC to state-of-the art native IM-HRMS (high resolution IM, CIU) to characterize the different mAbs isomers and variants (size, charge and hydrophobic); 2) Evaluate the possibilities offered by new generation high resolution IM-MS instrumentaition for more accurate conformational characterisation of mAb-formats.

Application deadline: To receive full consideration, applications must be submitted before 13 May 2024.

DC5: Development of IM-HRMS technology for vaccine and gene therapy vector characterisation

Waters (legal name: Micromass UK Ltd.) (WATERS), MS Research

Wilmslow, United Kingdom

Supervisor: Dr. Jakub Ujma

1) Develop a new analytical method to examine vectors used in vaccines and gene therapy to accelerate deployment of vaccine and gene therapy products; 2) Establish what instrumental performance (resolving power, sensitivity, reproducibility, analysis time) is “fit-for-purpose” in vaccine/gene therapy quality assurance laboratory. Once critical instrumental performance attributes are verified, further research will be undertaken to improve them as necessary. 3) Measurement of the ratio of empty and gene-containing capsids.

DC6: Unravelling the complexity of the sebum lipidome and the modulation of protein structure by lipids found within

University of Manchester (UNIMAN), Michael Barber Centre for Collaborative Mass Spectrometry

Manchester, United Kingdom

Supervisor: Prof. Perdita Barran

1) Characterise the complex lipids found in sebum, and develop a robust pipeline for analysis; 2) Identify the lipids that are robust biomarkers of high abundance and determine standard lipids that can be used to provide a targeted assay; 3) Examine how such lipids alter the structure of the protein alpha synuclein; 4) Apply optimised multicomponent workflows to quantify features in proteomic and lipidomic sebum extracts with use of standard yeast reference material.

DC7: High-sensitivity and multimodal trapped ion mobility mass spectrometry

University Hospital Jena (UKJ), Faculty of Medicine

Jena, Germany

Supervisor: Jun.-Prof. Florian Meier-Rosar

1) Analyse the two-dimensional ion mobility vs. mass-to-charge data space for peptides and lipids, in particular with regards to the calibration of collision cross section values and in comparison to other types of IM-HRMS technology; 2) Establish an efficient and scalable sample preparation protocol to extract lipids and proteins from the very same biological sample down to a single cell; 3) Develop advanced “parallel accumulation – serial fragmentation” (PASEF) data acquisition methods.

Application deadline: To receive full consideration, applications must be submitted before 30 April 2024.

DC8: IM-HRMS approaches for increasing confidence in the assessment of contaminants of emerging concern in indoor environment and humans

Universiteit Antwerpen (UAntwerpen), Department of Pharmaceutical Sciences

Antwerpen, Belgium

Supervisor: Prof. Dr. Adrian Covaci

1) Develop LC-DTIM-HRMS approaches for the broad screening of CECs present in the indoor environment and humans. 2) Deliver new experimental methods for CCS database generation for compounds associated with hazardous environmental properties. 3) Increase the knowledge on CECs regarding their distribution in the indoor environment and humans.

Application deadline: To receive full consideration, applications must be submitted before 30 March 2024.

DC9: Integrating IM into NTS workflows: advancing food safety and understanding of exposure

Oniris VetAgroBio – Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation (ONIRIS), LABERCA

Nantes, France

Supervisor: Dr. Gaud Dervilly

1) Develop NTS software tool to support chemical risk assessment of the exposome. 2) Create a robust and dynamic approach to deliver a vendor-independent CCS database for NTS using CECs associated with public health concerns (Persistent Organic Pollutants, Endocrine Disruptors), 3) Increase the performance and user-friendliness of high-throughput IM-HRMS nontarget screening (NTS) workflows.

DC10: Establishing Measurement Standards for Small Molecule Bioanalytical Methods Based on Ion Mobility-Mass Spectrometry

University of Natural Resources and Life Sciences (BOKU), Department of Chemistry

Vienna, Austria

Supervisor: Assoc. Prof. Tim Causon

1) Establish new dedicated measurement standards based on materials of biotechnological origin for broad application in small molecule analysis using commercial and non-commercial IM-HRMS technology; 2) Develop robust procedures for preparation of materials based on new reference samples derived from a recognised industrially relevant yeast (Pichia pastoris); 3) Optimise production of each material to ensure broadest analytical coverage in terms of m/z, CCS, and ensuring applicability within relevant analytical conditions, i.e. polarity, mode of chromatography; 4) Establish the new materials within analytical workflows encompassing a range of small molecule applications across all major commercial IM-HRMS instruments within MobiliTraIN.

Application deadline: To receive full consideration, applications must be submitted before 30 April 2024.

DC11: Protein and Polysaccharide Standards for Energy-Resolved IMS and CIU Experiments

Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy

Berlin, Germany

Supervisor: Prof. Dr. Kevin Pagel

The aim of the particular project is the development of a standardisation strategy for activation energy-resolved ion mobility experiments such as collision-induced unfolding (CIU). Technically this will involve the chemical synthesis of suitable peptide models and their subsequent analysis using ion mobility instruments from different vendors. This includes:

Chemical synthesis of suitable peptides displaying gas-phase unfolding and dissociation behavior over a wide range of energy during mass spectrometric analysis.
In-depth characterisation of energy-dependent processes in the gas phase using different instruments.
Application of the obtained energy scale to inter-laboratory protein CIU studies.

Application deadline: To receive full consideration, applications must be submitted before 11 March 2024.

DC12: Molecular simulation of macromolecules in IM-MS

Uppsala University (UU), Department of Chemistry

Uppsala, Sweden

Supervisor: Erik Marklund

1) Provide an assessment of the strength of salt-bridges in the gas phase in order to better predict the protonation of electrosprayed macromolecules, and evaluate the importance of polarization, which is often omitted in gas-phase MD simulations. 2) Develop and implement CCS-restraints in MD simulations, restricting the simulations to explore conformations consistent with experimental CCSs. 3) Benchmark the CCS restraints against experimental data and apply it to selected proteins from the consortium.

DC13: Leveraging ion mobility spectrometry for epitranscriptomics

Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche en Cancérologie de Montpellier (IRCM)

Montpellier, France

Supervisor: Dr. Alexandre David

1) Transpose workflows for bottom-up epitranscriptomics (analysis of RNA modifications) on an ion mobility-Q-TOF platform, inspired by workflows for bottom-up proteomics; 2) Establish what are the advantages of ion mobility separation (a) in terms of filtering and throughput and (b) in terms of structural insight on the modifications themselves or systematic effects of modifications on oligonucleotide structures. 3) Apply this knowledge in cancer biology: get novel insight into the effect of tRNA modifications in cancer, in particular cancer adaptation (metastasis and therapy).

Application deadline: To receive full consideration, applications must be submitted before 20 May 2024.