PXD020514

PXD020514 is an original dataset announced via ProteomeXchange.

Title	An Optimised Proteomics Workflow for the Detection of Small Proteins.
Description	Small 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.
HostingRepository	PanoramaPublic
AnnounceDate	2020-09-08
AnnouncementXML	Submission_2020-09-08_09:35:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Juergen Bartel
SpeciesList	scientific name: Bacillus subtilis; NCBI TaxID: 1423;
ModificationList	Deamidated; Gln->pyro-Glu; Carbamidomethyl; Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-22 15:32:45	ID requested
⏵ 1	2020-09-08 09:35:39	announced

Bartel J, Varadarajan AR, Sura T, Ahrens CH, Maa, ß S, Becher D, Optimized Proteomics Workflow for the Detection of Small Proteins. J Proteome Res, 19(10):4004-4018(2020) [pubmed]

submitter keyword: proteogenomics, Bacillus subtilis, SEPs, sProteins, Lys-C, small protein enrichment, PRM

Dörte Becher
contact affiliation	Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Juergen Bartel
contact affiliation	University of Greifswald, Center of Functional Genomics of Microbes, Institute of Microbiology, Department of Microbial Proteomics
contact email	juergen.bartel@uni-greifswald.de
dataset submitter

Panorama Public dataset URI