| title | description | published | date | tags | editor | dateCreated |
|---|---|---|---|---|---|---|
The Archaeal Proteome Project (ArcPP) |
The Archaeal Proteome Project (ArcPP) is a community effort that works towards a comprehensive analysis of archaeal proteomes. |
true |
2020-09-17 15:08:53 UTC |
reference, community, archaea, data capture, database, resource, proteomes, browser, protein, proteomics, model organism, data export, analysis tool, haloferax volcanii |
markdown |
2020-07-01 18:12:33 UTC |
ArcPP collects a diverse set MS data sets, uses state-of-the-art bioinformatic tools for their comprehensive analysis and expert knowledge from a broad range of fields for the interpretation of results. Starting with the model archaeon Haloferax volcanii, we have:
• Reanalyzed more than 23 Mio. spectra • Optimized the analysis using parameter sweeps, multiple search engines implemented in Ursgal, and the combination of results through the combined PEP approach • Thoroughly controlled false discovery rates for high confidence protein identifications using the picked protein FDR approach and limiting FDR to 0.5% • Identified more than 40k peptides, corresponding to 2,930 proteins (>72% of the proteome) with a median sequence coverage of 51%. {.is-info}
- ArcPP Main Page {.links-list}
- The website allows users to browse data. It is well designed and easy to use.
- Currently the website only has the completed proteome and data for Haloferax volcanii, but the goal of the developers is to expand the database with additional Archaeal proteomes.
- Data files can be downloaded for further processing.
- All scripts used in proteome analysis can be found on the GitHub page.
- "Please contact us with any questions, contributions or issues. Feel free to open issues and pull request on our GitHub page or contact us at [email protected]"
- ArcPP Help GitHub Page {.links-list}
- Schulze, S., Adams, Z., Cerletti, M., De Castro, R., Ferreira-Cerca, S., Fufezan, C., ... & Legerme, G. (2020). The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nature Communications, 11(1), 1-14. {.grid-list}