Dataset Open Access

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Schulze, Stefan

Data collector(s)
Adams, Zachary; Cerletti, Micaela; De Castro, Rosana; Ferreira-Cerca, Sébastien; Giménez, María Inés; Hippler, Michael; Jevtic, Zivojin; Knüppel, Robert; Legerme, Georgio; Lenz, Christof; Marchfelder, Anita; Maupin-Furlow, Julie; Paggi, Roberto A.; Pfeiffer, Friedhelm; Poetsch, Ansgar; Urlaub, Henning
Data curator(s)
Fufezan, Christian
Project manager(s)
Pohlschroder, Mechthild

Modern proteomics approaches can explore whole proteomes within a single mass spectrometry (MS) run. However, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and expertise needed from a diverse array of fields. In particular, in the field of microbiology, efforts to combine large-scale proteomic datasets have so far largely been missing. Thus, despite their relatively small genomes, the proteomes of most archaea remain incompletely characterized. This in turn undermines our ability to gain a greater understanding of archaeal cell biology.

Therefore, we have initiated the Archaeal Proteome Project (ArcPP), a community effort that works towards a comprehensive analysis of archaeal proteomes. Starting with the model archaeon Haloferax volcanii, using state-of-the-art bioinformatic tools, we have:

  • reanalyzed more than 23 Mio. spectra
  • optimized the analysis using parameter sweeps, multiple search engines implemented in Ursgal, and the combination of resultsthrough 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 2930 proteins (>72% of the proteome) with a median sequence coverage of 51%.

Benefiting from the established bioinformatic infrastructure, we will follow up on this analysis focusing on H. volcanii proteogenomics as well as the characterization of various post-translational modifications. Furthermore, ArcPP will integrate quantitative results obtained from the individual datasets in order to identify common regulatory mechanisms. These studies on the H. volcanii proteome can serve as a blueprint for comprehensive proteomic analyses performed on a diverse range of archaea and bacteria.

 

Updates version 1.1.0:
- Natrialba magadii results are included in PXD009116.zip

Files (3.4 GB)
Name Size
ArcPP_FDR_summary.pkl
md5:f4fd07e2b0ad0dd143642a5a4abf92a1
5.1 MB Download
ArcPP_results_peptides.csv
md5:957afa0a8d30323fb35a4b21f500dedd
47.3 MB Download
ArcPP_results_predicted_CS.csv
md5:0079710b440edba5491b92cd172a52ae
36.1 kB Download
ArcPP_results_proteins.csv
md5:c7c4722ed0dee3cfde7caa1b2569cc99
3.1 MB Download
ArcPP_results_PSMs.csv
md5:94752fdff390b1c19d2d2551294fa862
571.2 MB Download
ArcPP_summarized_results.pkl
md5:fcf6d47a885c7763ab655ee470d7bb99
783.4 MB Download
Haloferax_volcanii_ArcPP_20190606_uniprot.fasta
md5:3a1bdf65fd02e0ab14cdc18a15b9cfa4
1.4 MB Download
Haloferax_volcanii_ArcPP_20190606_uniprot_cRAP_target_decoy_gluc.fasta
md5:bc0663da2ec8f3df84ba31fafd6c01b7
3.0 MB Download
Haloferax_volcanii_ArcPP_20190606_uniprot_cRAP_target_decoy_trypsin.fasta
md5:5439b904da6e4baeb07f1848d453f974
3.0 MB Download
PXD000202.zip
md5:cb4ad3d5ba5c3fb72a395c2420a484c4
12.9 MB Download
PXD006877.zip
md5:4e7c2aa9839384c8323279d56f967796
241.9 MB Download
PXD007061.zip
md5:6741bda2d135b9113d682fdff14ce784
374.1 MB Download
PXD009116.zip
md5:644476cc94cfa4093704a63fc9dfcdb7
136.5 MB Download
PXD010824.zip
md5:d02b2258137140b24ee2b5cb5de7a132
27.8 MB Download
PXD011012.zip
md5:f2345483604f698628fefb8acacde2e4
566.9 MB Download
PXD011015.zip
md5:64e62d282f273746626631e2303df394
11.4 MB Download
PXD011050.zip
md5:54a32835ca7938e10fe4cdd806e84ac9
46.8 MB Download
PXD011056.zip
md5:6f4ef35e329d7dd72c0d4308439da51e
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PXD011218.zip
md5:6ac59050bebb3515c2458436f13d7fde
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PXD013046.zip
md5:ce16fc939a0ae9134fb04ae3c3d3bb9d
383.8 MB Download
PXD014974.zip
md5:574bdab57cfe4396f02acfc0109360e4
12.7 MB Download
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