Structural Characterization of Proteins and Protein Complexes by Hydrogen-Deuterium Exchange and Hydroxyl Radical Footprinting Centre for Genomic Regulation (CRG) in Spain

This fully funded PhD position at the Centre for Genomic Regulation (CRG) offers an exciting opportunity to advance structural proteomics through the development and optimization of hydrogen–deuterium exchange (HDX) mass spectrometry and hydroxyl radical footprinting (FPOP) experiments. The research aims to integrate ion mobility traces into data acquisition, improving sample preparation, MS acquisition strategies, and downstream data processing for high-confidence structural insights into protein dynamics.

The doctoral candidate will focus on optimizing robotic sample preparation for reliable and reproducible handling, tuning UPLC separation methods, and adjusting timsTOF instrument parameters for robust quantitative MS data. Data processing will involve developing scripts to convert raw files into text formats suitable for downstream analysis, followed by manual validation to establish benchmarks for subsequent AI-driven approaches. Visualization strategies will be designed to map HDX and FPOP results onto PDB structures, enhancing the interpretability of structural proteomics experiments.

The project will deliver reliable software and workflows for HDX and FPOP data processing, enabling streamlined interpretation of complex datasets. Outcomes will enhance understanding of protein structure and dynamics in basic research, while also providing methods with potential application in pharmaceutical R&D and biomanufacturing.

Doctoral training includes international secondments: a two-month placement at CRG in year 1 focusing on targeted MS acquisition methods for structural proteomics; a one-month secondment at FHOOE in year 2 to redesign search engine workflows for FPOP data analysis; and a one-month placement at Bruker in year 3 to implement developed tools into commercial software, bridging academic innovation with industrial applications.

The ideal candidate will have an interest in structural proteomics, mass spectrometry, and computational data processing, with strong analytical skills and motivation to work at the interface of experimental method development and data interpretation. The position is open to applicants of any nationality, subject to the MSCA mobility rule: candidates must not have resided or carried out their main activity in the host country for more than 12 months in the 3 years immediately before recruitment.

Funding is provided as part of a Marie Skłodowska-Curie Doctoral Network (MSCA-DN), including full salary, mobility allowance, and family allowance (where eligible) for 36 months. Apply through the ProtAIomics website, where eligibility criteria and the application form are available online. The deadline for applications is April 9, 2026.