PXD029391-2

PXD029391 is an original dataset announced via ProteomeXchange.

Title	Hidden in plain sight; challenges in proteomics detection of small ORF-encoded polypeptides.
Description	Genomic studies of bacteria have long pointed towards widespread prevalence of small open reading frames (sORFs) encoding for short proteins, less than 100 amino acids in length. Despite the mounting genomic evidence of their robust expression, little progress has been made in their mass spectrometry-based validation. Various blanket statements have been used to explain this discrepancy with the potentially low expression levels and protein instability being put forward most often. In this study we provide the first systemic investigation of the challenging nature of proteomic detection of such small proteins. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics is interrogated to provide the first evidence-based study of SEP detectability. Moreover, a large scale proteomics and genomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used to further support our in silico analysis. This integrative riboproteogenomic approach is used to provide a data-driven census of small proteins expressed by S. Typhimurium across growth phases and infection-relevant conditions. Taken together our study delineates current limitations in proteomics based validation of novel small proteins currently missing from bacterial genome annotations.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:03:02.866.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	2021-10-28 01:53:11	ID requested
1	2023-07-20 11:04:11	announced
⏵ 2	2023-11-14 09:03:03	announced	2023-11-14: Updated project metadata.
3	2024-10-22 05:55:19	announced	2024-10-22: Updated project metadata.

Fijalkowski I, Willems P, Jonckheere V, Simoens L, Van Damme P, Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides. Microlife, 3():uqac005(2022) [pubmed]

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

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/2023/07/PXD029391

PRIDE project URI

• PRIDE
  1. PXD029391
     1. Label: PRIDE project
     2. Name: Hidden in plain sight; challenges in proteomics detection of small ORF-encoded polypeptides.