PXD016298-2

PXD016298 is an original dataset announced via ProteomeXchange.

Title	Small proteins in a simplified human gut microbiome
Description	Small proteins (sProteins) with a size of 100 amino acids and less are involved in major biological processes and play an important role in different bacteria. Despite the increasing interest in them, the data on sProteins in bacterial communities, like the human gut microbiome is sparse. A reason for this is the technical challenge in the detection and identification of sProteins using bottom-up proteomics. In this study, we are using the simplified human gut microbiome (SIHUMIx) as model system of the human gut microbiome to detect sProteins and to compare different sProtein enrichment methods. We observed that with our tested methods, the C8-cartridge enrichment resulted in the highest number of detected sProteins (n=295) with high reproducibility among replication analysis. However, in order to further increase the total number of sProteins, the combination of C8 cartridge enrichment with GelFree enrichment is favored because the latter complemented n=48 more sProteins compared to the C8 cartridge approach resulting in n= 343 sProteins. Among all detected sProteins we were able to identify 79 so far uncharacterized sProteins, with no described protein evidence in the current released database. In total, 34 of those uncharacterized sProteins are localized in gene clusters conserved between different bacteria species allowing functional predictions. This study improves the assessment of sProtein detection and enables their functional characterization in future experiments.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:37.865.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Erysipelatoclostridium ramosum DSM 1402; NCBI TaxID: 445974; scientific name: Anaerostipes caccae DSM 14662; NCBI TaxID: 411490; scientific name: Bifidobacterium longum NCC2705; NCBI TaxID: 206672; scientific name: Clostridium butyricum DSM 10702; NCBI TaxID: 1316931; scientific name: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); NCBI TaxID: 226186; scientific name: Escherichia coli str. K-12 substr. MG1655; NCBI TaxID: 511145; scientific name: Blautia producta ATCC 27340 = DSM 2950; NCBI TaxID: 1121114; scientific name: Lactobacillus plantarum subsp. plantarum; NCBI TaxID: 337330;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-15 05:53:16	ID requested
1	2020-01-07 16:07:30	announced
⏵ 2	2024-10-22 04:59:38	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2019.103604;

Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M, Enrichment and identification of small proteins in a simplified human gut microbiome. J Proteomics, 213():103604(2020) [pubmed]

curator keyword: Biological

submitter keyword: SIHUMIx,small proteins, LC-MS/MS, metaproteomics

Nico Jehmlich
contact affiliation	Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 4767
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016298
     1. Label: PRIDE project
     2. Name: Small proteins in a simplified human gut microbiome