PROTrEIN (www.protrein.eu) is a European Innovative Training Network composed of 11 beneficiaries, and 6 partner organizations, from the academic and non-academic sectors (including two SMEs and two large companies).
The network’s mission is to train a new generation of computational proteomics researchers by providing them an inter-sectoral and interdisciplinary set of skills to tackle the main challenges in the field and improve their future employability.
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Subproject 7: (Host: Institute of Pharmacology and Structural Biology - CNRS-IPBS, Toulouse, France)
Title: Development of smart acquisition methods using real-time control of instruments and machine learning
Objectives: Develop intelligent data acquisition workflows to enhance proteomic analytical depth. While global MS acquisition methods based on DDA enable the direct, large-scale and unbiased analysis of complex samples, low-abundant proteins remain undetected in such single-run measurements. Approaches such as PRM or DIA take advantage of previously acquired information (e.g. validated peptide sequence matches, libraries…) to improve the detection of low-abundant molecules during analysis of the samples. The problem of retention time (RT) variability complicates the efficient use of previously collected data when programming scheduling methods to specifically detect at high sensitivity many low abundant proteins (high-throughput PRM). We plan to develop new open-source software solutions for real-time control of MS acquisition in order to improve the implementation and multiplexing of high sensitivity PRM measurements, based on optimized RT prediction.
Methodology: The ESR will develop new open-source software solutions for real-time control of instruments, integrated with the MS-Angel tool for the automation of data processing tasks and subsequent triggering of customized acquisition methods. He will also evaluate machine learning algorithms and existing solutions (e.g. Prosit) to improve the parameters of peptides fragmentation.
Required skills:
Knowledge of data acquisition by mass spectrometry
C# programming language (experimented)
Expected Results: An open-source framework facilitating the development of new real-time and smart acquisition methods, improving the throughput of PRM assays.
Planned Secondments:
Host: TUM P6 (Germany), Duration: 3 Months; When: Year 2; Goal: Methods optimization with Prosit.
Host: EKUT P8 (Germany), Duration: 1 Month; When: Year 3; Goal: Integration with OpenMS.
Enrolment in doctoral programs: PhD in Bioinformatics from University of Toulouse
Application Procedure:
An application is solely possible via the PROTrEIN application form: http://protrein.eu/call-for-applicants/
Applications must be in English. Applicants may indicate 3 ESR Projects which they would like to work on, ranking them in order to preference. Uploading reference letters is not mandatory, but applicants should be aware that referees will be automatically contacted after submission and receive a questionnaire. Candidates must provide all information before the deadline. Candidates should ensure that referees answer the questionnaire.
Application deadline: 28 February 2021
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About CNRS-IPBS:
The Centre National de la Recherche Scientifique (CNRS) is a publicly funded research organization, under the authority of the French Ministry of Research, and is the largest of several French research organizations with the legal status of Public Scientific and Technological Institution. The Institute of Pharmacology and Structural Biology (IPBS) is a world-renowned research center in biology. It is located in Toulouse, France, and it is affiliated with CNRS and the University of Toulouse. Its primary objective is the identification, characterization and exploitation of novel therapeutic targets in the fields of Cancer, Infection and Inflammation.
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