Periodic Reporting for period 1 - SPIDoc's (The Next Generation MS SPIDoc’s)
Período documentado: 2023-09-01 hasta 2025-08-31
SPIDocs is an interdisciplinary and intersectoral doctoral network comprising 7 Beneficiaries and 7 associated partners, and 10 Doctoral Candidates (DCs).
Among the partners, three are industry partners, of which one is a beneficiary hosting two DCs,
SPIDocs developed ad-hoc training programme covering the different disciplines represented in the network, aiming to fill the gap in the interdisciplinary training of the next generation of scientists.
All partners actively contribute to the training programme, either with courses and/or by hosting secondments.
The engagement and collaboration among all partners is well established and based on the previous MS SPIDOC project (H2020, FETOPEN-01-2016-2017).
By combining a theoretical approach via molecular dynamics and quantum mechanic simulations with instrument development SPIDoc's aims to contribute to the understanding of proteins structures for a broad range of applications, like structural virology. The interdisciplinary framework requires different expertise, for which the SPIDocs training courses are designed. The SPIDoc's doctoral candidates acquire a common understanding of the scientific fields (theory, instrumentation and application) and a deeper knowledge in the field of their specific project.
SPIDoc’s addresses the following lead and dependent objectives:
1. Training the next generation of DCs capable of understanding and applying theory, virology and instrumentation to their own research questions.
2. Theoretical understanding of gas phase structures of ions and the nature of light-matter interactions relevant for instrumentation development and applications.
3. Development of MS components specifically tuned to large viral assemblies and adapt the MS SPIDOC design into a versatile tool kit for other light sources and applications.
4. Application of structural approaches including MS and light sources to probe virus - ligand / -host interactions on various size and time scales – from local electronic transitions to large complexes such as viral particles.
Among the partners, three are industry partners, of which one is a beneficiary hosting two DCs,
SPIDocs developed ad-hoc training programme covering the different disciplines represented in the network, aiming to fill the gap in the interdisciplinary training of the next generation of scientists.
All partners actively contribute to the training programme, either with courses and/or by hosting secondments.
The engagement and collaboration among all partners is well established and based on the previous MS SPIDOC project (H2020, FETOPEN-01-2016-2017).
By combining a theoretical approach via molecular dynamics and quantum mechanic simulations with instrument development SPIDoc's aims to contribute to the understanding of proteins structures for a broad range of applications, like structural virology. The interdisciplinary framework requires different expertise, for which the SPIDocs training courses are designed. The SPIDoc's doctoral candidates acquire a common understanding of the scientific fields (theory, instrumentation and application) and a deeper knowledge in the field of their specific project.
SPIDoc’s addresses the following lead and dependent objectives:
1. Training the next generation of DCs capable of understanding and applying theory, virology and instrumentation to their own research questions.
2. Theoretical understanding of gas phase structures of ions and the nature of light-matter interactions relevant for instrumentation development and applications.
3. Development of MS components specifically tuned to large viral assemblies and adapt the MS SPIDOC design into a versatile tool kit for other light sources and applications.
4. Application of structural approaches including MS and light sources to probe virus - ligand / -host interactions on various size and time scales – from local electronic transitions to large complexes such as viral particles.
WorkPackage 1: Theory
SPIDoc's applies the theoretical study of protein orientation for single particle imaging experiments by quantum mechanics/molecular modelling and hybrid-molecular dynamics simulations. Additionally, a rigid rotor model is used to study the influence of protein dipole and field strength to predict protein orientation.
The work of WP1 is carried out by DC6 and DC7 (both at Uppsala University).
WorkPackage 2: Instrumentation
The development of MS components, as well as the adaption of the prototype developed within the MS SPIDOC project, contributes to the better characterization of small and large protein species. The instrument development has the main feature of versatility to be adapted to different applications and beamline. Specficially, the design of an optimized MS-based sample delivery system results in the TXI prototype which has been tested at the beamline. Along with instrument development, an important aspect to be considered is data analysis, which is addressed by the development of a software package for native MS data analysis.
The work of WP2 is carried out by DC1 (University of Lübeck), the DC9 and DC10 (both at MS Vision).
WorkPackage 3: Application
The different theoretical methods and instruments are applied to the structural approaches for the study of biological systems. Near-edge X-ray absorption mass spectrometry is used to investigate the properties of proteins related to Alzheimer´s disease, while the structural stability of the protruding domain of the norovirus capsid protein is analysed with a combination of IM-MS, collision-, temperature-, and laser-induced unfolding. The structure and stability of proteins in the gas phase are also addressed by the FTICR mass spectrometer application and the dynamic behaviour of viral systems, specifically on self-assembly and disassembly, and protein–protein interactions is carried out on SARS-CoV-2 non-structural proteins.
The work of WP3 is carried out by DC2 (University of Lübeck), DC3 (Vrije Universiteit Amsterdam), DC4 (Deutsches Elektronen-Synchrotron), DC5 (University Lyon 1 Claude Bernard), DC8 (Institute of Microbiology of the Czech Academy of Sciences).
WorkPackage 4: Training
The SPIDoc's training programme covers the three scientific workpackages including courses on molecular dynamics simulations, instruments' development, sample preparation, as examples. Additionally to the scientific courses, the training programme offers courses on 'green science', diversity and microaggression at the workplace, research integrity and data management, as examples. Participation to conferences is also part of the training programme, as well as the organization of outreach events.
SPIDoc's applies the theoretical study of protein orientation for single particle imaging experiments by quantum mechanics/molecular modelling and hybrid-molecular dynamics simulations. Additionally, a rigid rotor model is used to study the influence of protein dipole and field strength to predict protein orientation.
The work of WP1 is carried out by DC6 and DC7 (both at Uppsala University).
WorkPackage 2: Instrumentation
The development of MS components, as well as the adaption of the prototype developed within the MS SPIDOC project, contributes to the better characterization of small and large protein species. The instrument development has the main feature of versatility to be adapted to different applications and beamline. Specficially, the design of an optimized MS-based sample delivery system results in the TXI prototype which has been tested at the beamline. Along with instrument development, an important aspect to be considered is data analysis, which is addressed by the development of a software package for native MS data analysis.
The work of WP2 is carried out by DC1 (University of Lübeck), the DC9 and DC10 (both at MS Vision).
WorkPackage 3: Application
The different theoretical methods and instruments are applied to the structural approaches for the study of biological systems. Near-edge X-ray absorption mass spectrometry is used to investigate the properties of proteins related to Alzheimer´s disease, while the structural stability of the protruding domain of the norovirus capsid protein is analysed with a combination of IM-MS, collision-, temperature-, and laser-induced unfolding. The structure and stability of proteins in the gas phase are also addressed by the FTICR mass spectrometer application and the dynamic behaviour of viral systems, specifically on self-assembly and disassembly, and protein–protein interactions is carried out on SARS-CoV-2 non-structural proteins.
The work of WP3 is carried out by DC2 (University of Lübeck), DC3 (Vrije Universiteit Amsterdam), DC4 (Deutsches Elektronen-Synchrotron), DC5 (University Lyon 1 Claude Bernard), DC8 (Institute of Microbiology of the Czech Academy of Sciences).
WorkPackage 4: Training
The SPIDoc's training programme covers the three scientific workpackages including courses on molecular dynamics simulations, instruments' development, sample preparation, as examples. Additionally to the scientific courses, the training programme offers courses on 'green science', diversity and microaggression at the workplace, research integrity and data management, as examples. Participation to conferences is also part of the training programme, as well as the organization of outreach events.
The impact of SPIDoc’s can be seen on different aspects:
- Development of advanced instrumentation for specific biological applications. The peculiarity of the instruments resides in their modularity and adaptation to different beamlines, allowing sustainability and versatility of applications;
- Standardization of data analysis methods for native MS filling a current scientific gap and relevant for data reusable;
- Combination of technologies allowing a deeper understanding of protein structures and properties, including viral particles, contributing to the understanding of drug targets impacting on health;
- Communication to the civil society beyond the scientific projects is achieved by the second edition of the comics, as follow up to the previous MS SPIDOC project. With the comics, SPIDocs will go beyond communicating the scientific projects, as it will include the challenges and the team work required in research;
- The interdisciplinary and intersectoral training of DCs will result in young scientists with a new professional profile, with knowledge and application in different scientific fields and sectors.
- Dissemination of the scientific results is reached by the participation to national and international conferences with more than 30 oral presentations and more than 15 poster presentations, and 4 scientific peer-reviewed publications including a journal cover and corresponding press releases on the institutes' websites. Communication and outreach includes events, such as the 'Career Day', as part of the training program and allowing the DCs to explore different career paths and giving visibility to SPIDoc's.
- Development of advanced instrumentation for specific biological applications. The peculiarity of the instruments resides in their modularity and adaptation to different beamlines, allowing sustainability and versatility of applications;
- Standardization of data analysis methods for native MS filling a current scientific gap and relevant for data reusable;
- Combination of technologies allowing a deeper understanding of protein structures and properties, including viral particles, contributing to the understanding of drug targets impacting on health;
- Communication to the civil society beyond the scientific projects is achieved by the second edition of the comics, as follow up to the previous MS SPIDOC project. With the comics, SPIDocs will go beyond communicating the scientific projects, as it will include the challenges and the team work required in research;
- The interdisciplinary and intersectoral training of DCs will result in young scientists with a new professional profile, with knowledge and application in different scientific fields and sectors.
- Dissemination of the scientific results is reached by the participation to national and international conferences with more than 30 oral presentations and more than 15 poster presentations, and 4 scientific peer-reviewed publications including a journal cover and corresponding press releases on the institutes' websites. Communication and outreach includes events, such as the 'Career Day', as part of the training program and allowing the DCs to explore different career paths and giving visibility to SPIDoc's.