The ProteoToul team is involved in the development of several bioinformatics tools for bottom-up and top-down mass spectrometry data analysis:

  • Proline (http://www.profiproteomics.fr/proline) [1]: a new software suite for the processing of bottom-up datasets. It offers efficient and competitive performance for the analysis of label-free DDA datasets (see the related publication [1] for a comparison with MaxQuant). Proline is developed through a collaborative project of the French proteomics infrastructure (ProFI).
  • HDX-Viewer [2]: a simple web interface for the visualization of results obtained from “Hydrogen Deuterium Exchange” (HDX) experiments.
  • VisioProt-MS [3]: a graphical interface to visualize and analyze intact protein and top-down proteomics data.

Demo versions of these tools are available from the “Mass Tools” portal (https://masstools.ipbs.fr) hosted by the IPBS.

The source codes of these projects are available from their respective Github repositories:
https://github.com/profiproteomics
https://github.com/mlocardpaulet/VisioProt-MS
https://github.com/david-bouyssie/hdx-viewer

[1] Bouyssié D, Hesse AM, Mouton-Barbosa E, Rompais M, Macron C, Carapito C, Gonzalez de Peredo A, Couté Y, Dupierris V, Burel A, Menetrey JP, Kalaitzakis A, Poisat J, Romdhani A, Burlet-Schiltz O, Cianférani S, Garin J, Bruley C. Proline: an efficient and user-friendly software suite for large-scale proteomics. Bioinformatics. 2020 May 1;36(10):3148-3155. doi: 10.1093/bioinformatics/btaa118. PMID: 32096818; PMCID: PMC7214047.

 

[2] Bouyssié D, Lesne J, Locard-Paulet M, Albigot R, Burlet-Schiltz O, Marcoux J. HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data. Bioinformatics. 2019 Dec 15;35(24):5331-5333. doi: 10.1093/bioinformatics/btz550. PMID: 31287496; PMCID: PMC6954641.

 

[3] Locard-Paulet M, Parra J, Albigot R, Mouton-Barbosa E, Bardi L, Burlet-Schiltz O, Marcoux J. VisioProt-MS: interactive 2D maps from intact protein mass spectrometry. Bioinformatics. 2019 Feb 15;35(4):679-681. doi: 10.1093/bioinformatics/bty680. PMID: 30084957; PMCID: PMC6378940.