PXD025297

PXD025297 is an original dataset announced via ProteomeXchange.

Title	Small protein enrichment improves proteomics detection of sORF encoded peptides.
Description	With the rapid growth in the number of sequenced genomes, genome annotation efforts became almost exclusively reliant on automated pipelines. Despite their unquestionable utility, these methods have been shown to underestimate the true complexity of the studied genomes, with small open reading frames (sORFs; ORFs shorter than 300 nucleotides) and, in consequence, their protein products (sORF encoded polypeptides or SEPs) being the primary example of a poorly annotated and highly underexplored class of genomic elements. With the advent of advanced translatomics such as ribosome profiling, reannotation efforts have progressed a great deal in providing translation evidence for numerous, previously unannotated sORFs. However, proteomics validation of these riboproteogenomics discoveries remains challenging due to their short length and often highly variable physiochemical properties. In this work we evaluate and compare tailored, yet easily adaptable, protein extraction methodologies for their efficacy in facilitating the extraction and concomitantly proteomics detection of SEPs expressed in the prokaryotic model organism Salmonella Typhimurium. An optimized protocol for the enrichment and efficient detection of SEPs making use of the of amphipathic polymer amphipol A8-35 relying on the differential peptide versus protein solubility is suggested and compared with global extraction methods making use of chaotropic agents. Given the versatile biological functions the SEPs have been shown to exert, this work provides an accessible protocol for proteomics exploration of this fascinating class of small proteins.
HostingRepository	PRIDE
AnnounceDate	2021-10-07
AnnouncementXML	Submission_2021-10-07_00:44:56.081.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Igor Fijalkowski
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; NCBI TaxID: 216597;
ModificationList	monohydroxylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-09 03:50:54	ID requested
⏵ 1	2021-10-07 00:44:56	announced

Dataset with its publication pending

submitter keyword: Salmonella, Peptidomics, SEPs

Petra Van Damme
contact affiliation	iRIP Unit, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
contact email	petra.vandamme@ugent.be
lab head
Igor Fijalkowski
contact affiliation	Ugent
contact email	igor.fijalkowski@ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025297
     1. Label: PRIDE project
     2. Name: Small protein enrichment improves proteomics detection of sORF encoded peptides.