Last major publications
We are pleased and very proud to announce the publication of Proline in Bioinformatics.
Here, we present Proline, a robust software suite for analysis of MS-based proteomics data which collects, processes, allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency….
Feel free to try the software by downloading the zero installation version.
Although biomarkers are widely used, important limitations have been identified due to their lack of specificity. An a priori knowledge-based approach (i.e. based on mechanistic criteria specific to the genesis of a disease) that takes advantage of ever-increasing “omics” databases could be a powerful way to identify biomarkers, provided that scientists have access to computer tools to search the data even when they have little experience in programming or bioinformatics support.
Bouyssié D, Lesne J, Locard-Paulet M, Albigot R, Burlet-Schiltz O, Marcoux J. Bioinformatics. 2019 Jul 9. pii: btz550. doi: 10.1093/bioinformatics/btz550. With the advent of fully automated sample preparation robots for Hydrogen–Deuterium eXchange coupled to Mass...
ProFI interacts with IFB in the context of Elixir (see “On the international stage” section) but also at the national level. Christophe Bruley, responsible for the development of Proline [lien à mettre], is co-leader of an IFB action (Sharing of services with other national research support infrastructures).
1st FRISBI/ Profi Proteomics meeting
The 1st FRISBI/ProFI Proteomics meeting was held the 21 November, 2017 at CNRS Campus Gif-sur-Yvette The meeting was organised by FRISBI and Profi infrastructures with more than 70 participants from both communities.
A close collaboration has been established with PHENOMIN, the national infrastructure in mouse phenogenomics, to analyse signaling initiated at T-cell receptors (TCRs) in primary murine cells. Most of the studies performed up till now on TCR signaling pathways involved the use of immortalized cultured cell lines, such as Jurkat cells; the relevance of the findings with these models can be questioned. The ProFI and PHENOMIN infrastructures have come together to take on the challenge of performing studies directly on primary cells isolated from model animals. These studies focus on the precise and dynamic characterization of signaling initiated at the TCR using various murine models, in particular a range of transgenic mice each presenting a unique type of TCR which can be activated using peptides which will be recognized with varying affinities.
ProFI contact: Myriam Ferro
On the international stage
HUPO: Human Proteome Organization
ProFI is actively implicated in the C-HPP initiative (Chromosome-centric Human Proteome Project) managed by HUPO. This very ambitious project aims to systematically identify all the protein forms present in all tissues, cell type and fluids of the human body through the massive use of proteomics. It combines the efforts of over 25 national networks worldwide. The work of cataloguing the proteins expressed was organized by chromosome, and France was allocated responsibility for chromosome 14. This work was carried out in the context of a close collaboration with Swiss teams (coordinator Lydie Lane; chromosome 2). After a first publication (Carapito et al., 2015), our activity within C-HPP was followed by a new large study analysing proteins expressed in the human testis and sperm (coll C. Pineau; Vandenbrouck et al., 2016 ; Carapito et al., 2017). ProFI contacts: Yves Vandenbrouck, Christine Carapito
HUPO Bioinformatics Hub. Members of ProFI were at the initiative of the Bioinformatic Hub which is now a recurrent event at HUPO since 2015 and participate to the management of this gathering. The Bioinformatics Hub is a place where bioinformaticians gather together with three aims:
- to provide their advice, knowledge, and support to anyone with a relevant question;
- to discuss current issues and challenges in proteomics informatics with the entire community;
- to work on interesting, synergistic projects and to freely exchange tools, algorithms and know-how with each other, across all labs, seniorities and levels of experience. ProFI contacts: Yves Vandenbrouck, David Bouyssié
ProFI is also largely involved in the EuPA Bioinformatics Community (EuBIC). ProFI participated to the EuBIC kickoff meeting (Dortmund, December 2015) and was an actor of both the “Bioinformatics Bazar” (the equivalent of the HUPO “Bioinformatics hub”) during the EuPA 2016 congress and the 2017 EuBIC workshop. ProFI contact: David Bouyssié
ProFI is actively involved in the initiative launched by EuPA for the assessment of standards in proteomics (“EuPA standardisation” initiative). Fernando Corrales, coordinator of this initiative, actively sought out ProFI after having heard of our work and seen our publications related to the development of robust quantitative methods in label free proteomics (Ramus et al., 2016). We were involved in an inter-laboratory study of a complex protein sample which is used as a standard for the quantitative analysis of phosphoproteins. The results of this study was presented during the EuPA 2016 conference in a session dedicated to this initiative. ProFI contact: Odile Schiltz
ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. In that context, together with IFB (Institut Français de Bioinformatique) ProFI has been involved in brainstormings about the future of proteomics in ELIXIR (Vizcaino et al., 2017). ProFI contact: Myriam Ferro
Tools and methods for the community
The need to respond in a controlled manner to requests for scientific services or collaborations, the need to consolidate the quality of the expertise carried out by managing the skills of the staff concerned and the control of the instrumentation platforms led each node of ProFI to the implementation of an ISO 9001-type Quality Management System.
Each node of ProFI has obtained ISO 9001 and more recently the complementary NFX 50-900 certifications for quality standards. They have developed tools to store, share and manage data. All proteomic analyses and research projects are registered in a database. The corresponding files can be recovered at any time to follow their achievement status.
The aim of quality management is to improve the organization and traceability of the work carried out. It is based on a continuous improvement of the system. It relies on four interconnected actions making a cycle: plan, do, check, and act. This allows an efficient organization with defined objectives, actions that are implemented and verified, and results that are analyzed to define new objectives to achieve results improvement.