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PXD020514 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAn Optimised Proteomics Workflow for the Detection of Small Proteins.
DescriptionSmall open reading frame encoded proteins (SEPs) gained increasing interest during the last years due to their broad range of important functions in both, prokaryotes and eukaryotes. In bacteria, signalling, virulence or regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome studies is often low as classical methods are biased towards the identification of larger proteins. In the accompanying manuscript, we present a workflow that allows enhanced identification of small proteins compared to traditional protocols. For this aim, the steps of small protein enrichment, proteolytic digest and database search were reviewed and adjusted to the special requirement of SEPs. Enrichment by the use of small-pore-sized solid-phase material increased the number of identified SEPs by a factor of two and the utilisation of alternative proteases to trypsin reduced spectral counts for larger proteins. The application of the optimised protocol allowed the detection of 210 already annotated proteins up to 100 amino acids length, including 16 proteins below 51 amino acids in the Gram-positive model organism Bacillus subtilis. Moreover, 12% of all identified proteins were up to 100 amino acids which is a significant larger fraction than reported in studies involving traditional proteomics workflows. Finally, an integrated proteogenomics search database was applied to identify potentially novel SEPs. This submission contains PRM data generated in order to verify the identification of novel very small proteins in Bacillus subtilis. Three SEPs, which are 21, 26 and 42 amino acids long, respectively were successfully verified.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJuergen Bartel
SpeciesList scientific name: Bacillus subtilis; NCBI TaxID: 1423;
ModificationListDeamidated; Gln->pyro-Glu; Carbamidomethyl; Oxidation
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-22 15:32:45ID requested
12020-09-08 09:35:39announced
Publication List
Bartel J, Varadarajan AR, Sura T, Ahrens CH, Maaß S, Becher D, Optimized Proteomics Workflow for the Detection of Small Proteins. J Proteome Res, 19(10):4004-4018(2020) [pubmed]
Keyword List
submitter keyword: proteogenomics, Bacillus subtilis, SEPs, sProteins, Lys-C, small protein enrichment, PRM
Contact List
Dörte Becher
contact affiliationDepartment of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
contact emaildbecher@uni-greifswald.de
lab head
Juergen Bartel
contact affiliationUniversity of Greifswald, Center of Functional Genomics of Microbes, Institute of Microbiology, Department of Microbial Proteomics
contact emailjuergen.bartel@uni-greifswald.de
dataset submitter
Full Dataset Link List
Panorama Public dataset URI