<<< Full experiment listing

PXD031691-1

PXD031691 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSmall Proteome of Haloferax volcanii - Proteogenomic database search strategy
DescriptionThe small proteome has already been well explored in eukaryal and bacterial species, but so far, archaeal genomes have not yet been analysed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental information from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq) to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. Translation was demonstrated for 67% of the annotated small coding sequences by both methods. Annotation-independent data analysis allowed for the prediction of 47 sites of ribosomal engagement outside known coding regions by Ribo-seq, seven of whom correspond to the eight un-annotated small proteins identified by a similar independent analysis of proteomic data. We also present independent evidence in vivo for the translation of a subset of small proteins (comprising both previously annotated and newly identified), underlining the validity of our identification scheme. Moreover, several of these translated sORFs are conserved in Haloferax and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously expected and that the combined use of mass spectrometry to detect protein presence with Ribo-seq to inform on translation is a powerful tool for the discovery of new small protein-coding genes in diverse organisms. This data-set contains the search results obtained from an MS-Fragger search against six-frame genome translation-derived database that were mapped to the genome by Stephan Fuchs “Salt & Pepper” software suite for bacterial proteogenomics.
HostingRepositoryPRIDE
AnnounceDate2023-02-02
AnnouncementXMLSubmission_2023-02-01_16:09:43.992.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJuergenBartel
SpeciesList scientific name: Haloferax volcanii (Halobacterium volcanii); NCBI TaxID: 2246;
ModificationListiodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-02-15 08:44:50ID requested
12023-02-01 16:09:44announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: SEP, Archaea, sProtein, proteogenomics, database search,sORF, small protein enrichment, Top-down, ribosome profiling, Haloferax volcanii, small protein, proteolytic digest
Contact List
DörteBecher
contact affiliationUniversity of Greifswald, Institute for Microbiology, Department for Microbial Proteomics
contact emaildbecher@uni-greifswald.de
lab head
JuergenBartel
contact affiliationUniversity of Greifswald, Department for Microbial Proteomics
contact emailjuergen.bartel@uni-greifswald.de
dataset submitter
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/02/PXD031691
PRIDE project URI
Repository Record List
[ + ]