PXD017416-2

PXD017416 is an original dataset announced via ProteomeXchange.

Title	Optimised Workflow for the Proteomic 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 in eukaryotes. In bacteria, signalling, virulence or regulation of enzyme activities have been associated with this protein class. 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 rates 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 absolute numbers of identified SEPs by a factor of two and the application of alternative proteases to trypsin reduced spectral counts for larger proteins. The application of an integrated proteogenomics search database (iPtgxDB) in combination with the optimized protocol allowed the detection of several proteins not yet annotated in the reference genome of Bacillus subtilis. Finally, the identification of some of these missed proteins was validated by comparing their identifying spectra to those of synthetic peptides.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:13:14.026.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juergen Bartel
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	carbamoylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-06 04:14:18	ID requested
1	2020-10-12 07:13:16	announced
⏵ 2	2024-10-22 05:13:19	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.0c00286;

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]

curator keyword: Technical, Biological

submitter keyword: database search, small protein enrichment, SEPs,proteogenomics, Bacillus subtilis, sProteins, proteolytic digest

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

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/2020/10/PXD017416

PRIDE project URI

• PRIDE
  1. PXD017416
     1. Label: PRIDE project
     2. Name: Optimised Workflow for the Proteomic Detection of Small Proteins