Développement de nouveaux outils bioinformatiques pour l'exploitation des données de spectrométrie de masse en protéomique haut-débit

En biologie, la spectrométrie de masse est devenue l'outil incontournable pour l'identification des protéines. Associée à des techniques de séparation, elle est aussi utilisée pour mesurer la variation d'abondance des protéines entre plusieurs échantillons. Cependant, la très grande quantité et complexité des données liées à ce type d'analyse requièrent des programmes informatiques sophistiqués et adaptés. Mon travail de doctorat a consisté à répondre aux différentes problématiques liées à l'exploitation des données nanoLC-MS/MS, à savoir la validation des résultats d'identification ainsi que la quantification relative des protéines pour des approches mettant en œuvre ou non un marquage isotopique. Le logiciel MFPaQ, dont deux versions sont présentées dans ce document, en est le principal résultat. La version 3 intègre des fonctionnalités telle que la validation des données Mascot, la génération de listes non-redondantes de protéines et la quantification d'analyses ICAT. La version 4, évolution majeure du logiciel, incorpore des algorithmes adaptés à l'analyse quantitative de données MS sans marquage, ainsi que la gestion des stratégies de marquage SILAC et 14N/15N. Son utilisation a facilité la réalisation d'études protéomiques, dont certaines, auxquelles j'ai plus particulièrement participé, sont présentées. Afin de répondre aux futurs enjeux informatiques de la protéomique, j'ai entrepris dans un second temps le développement du logiciel Prosper, qui dispose d'une architecture d'organisation des données permettant de réaliser des requêtes croisées sur l'ensemble des échantillons analysés. Il constitue aussi un outil prototype pour l'élaboration de nouveaux algorithmes.In biology, mass spectrometry has become an indispensable tool for protein identification. Associated with separation techniques, it can also be used to measure the variation of protein abundance between different samples. However, due to the huge quantity and complexity of the data produced by this kind of analysis, sophisticated and suitable computer programs are needed. My PhD work was to address the different issues related to the processing of nanoLC-MS/MS data, namely the validation of the identification results, and the relative quantification of proteins using approaches based or not on isotopic labeling. The MFPaQ program, two versions of which are presented here, is the main result of this work. Version 3 includes features such as Mascot data validation, generation of non-redundant protein lists and quantification of ICAT analyses. Version 4, which represents a major upgrade of the software, incorporates additional algorithms for quantitative analysis of label-free MS data, as well as for the handling of the 14N/15N and SILAC labeling strategies. This bioinformatic tool has been used for various proteomic studies, some of which are discussed here. In order to meet future IT challenges in proteomics, I undertook later the development of the Prosper software, which is based on an optimized architecture for organizing data, and allows performing cross-queries on all analysed samples. It also constitutes a prototype tool for the development and evaluation of new algorithms

Variations sur Richard III

Petite vidéo amusée sur l’adaptation de Richard III par Thomas Jolly.Mischievous video on Thomas Jolly’s adaptation of Richard II

Proceedings of the EuBIC Winter School 2019

The 2019 European Bioinformatics Community (EuBIC) Winter School was held from January 15th to January 18th 2019 in Zakopane, Poland. This year’s meeting was the third of its kind and gathered international researchers in the field of (computational) proteomics to discuss (mainly) challenges in proteomics quantification and data independent acquisition (DIA). Here, we present an overview of the scientific program of the 2019 EuBIC Winter School. Furthermore, we can already give a small outlook to the upcoming EuBIC 2020 Developer’s Meeting

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato(Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration)and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome

A community proposal to integrate proteomics activities in ELIXIR

Computational approaches have been major drivers behind the progress of proteomics in recent years. The aim of this white paper is to provide a framework for integrating computational proteomics into ELIXIR in the near future, and thus to broaden the portfolio of omics technologies supported by this European distributed infrastructure. This white paper is the direct result of a strategy meeting on ‘The Future of Proteomics in ELIXIR’ that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes.   These discussions led to a list of priority areas in computational proteomics that would complement existing activities and close gaps in the portfolio of tools and services offered by ELIXIR so far. We provide some suggestions on how these activities could be integrated into ELIXIR’s existing platforms, and how it could lead to a new ELIXIR use case in proteomics. We also highlight connections to the related field of metabolomics, where similar activities are ongoing. This white paper could thus serve as a starting point for the integration of computational proteomics into ELIXIR. Over the next few months we will be working closely with all stakeholders involved, and in particular with other representatives of the proteomics community, to further refine this paper

A proteomics sample metadata representation for multiomics integration and big data analysis

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.publishedVersio

Critique vidéo de Richard III, William Shakespeare / Thomas Jolly (2016). Variations sur Richard III

Mischievous video on Thomas Jolly’s adaptation of Richard II