ProteoRE

Public Server:	ProteoRE Galaxy (FR)
Scope:	Domain Specific
Summary:	ProteoRE (Proteomics Research Environment)

Comments

"ProteoRE (Proteomics Research Environment) aims at centrally providing the proteomics community with an online research service enabling biologists/clinicians without programming expertise to **annotate and interpret** their proteomics data through the Web."
ProteoRE currently comprises tools (including graphical display) for:
Customary data manipulation (e.g. filtering, lists comparison, ID conversion…)
Protein list annotation (e.g. information retrieval from public resources - human species)
Functional analysis (e.g. GOterms frequencies, enrichment analysis) including graphical representation.
Pathway analysis (e.g. Reactome)
This version also includes Galaxy generic tools and some tools from the [GalaxyP project](https://usegalaxyp.org/) that should be of great help for people who want to (re)process their MS-based proteomics data (e.g. peptide/protein identification).
[ProteoRE tools in the Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/view/proteore)

Help and support: contact@proteore.org
Tutorial: [Annotating a protein list identified by LC-MS/MS experiments](http://proteore.org/u/proteore/p/proteore-tutorial-1-annotating-a-protein-list-identified-by-lc-msms-experiments)
Tutorial: [Biomarker candidate identification](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/tutorial.html)

Unregistered user: allocated storage space is limited to 20 Mb and is not conserved between sessions.
Registered user: up to 20 Gb per registered user

Combes, F., Loux, V., & Vandenbrouck, Y. (2021). [GO enrichment analysis for Differential Proteomics Using ProteoRE](https://doi.org/10.1007/978-1-0716-1641-3_11). In D. Cecconi (Ed.), Proteomics Data Analysis (pp. 179–196). Springer US. https://doi.org/10.1007/978-1-0716-1641-3_11
[Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework](https://doi.org/10.1007/978-1-4939-9164-8_18), Nguyen L., Brun V., Combes F., Loux V., Vandenbrouck Y. (2019) In: Brun V., Couté Y. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1959. Humana Press, New York, NY
[P17: ProteoRE, a Galaxy-based infrastructure for interpreting and exploring mass spectrometry-based proteomics data](http://sched.co/B8U9), [GCC2017](https://gcc2017.sched.com/) poster presentation, Lien Nguyen, Maud Lacombe, Sandra Dérozier, Lisa Perus, Olivier Rué, Florence Combes, Christophe Caron, Virginie Brun, Valentin Loux, Yves Vandenbrouck
ProteoRE tagged publications in the Galaxy Publication Library