PXD005074

PXD005074 is an original dataset announced via ProteomeXchange.

Title	Comparative Analysis of two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics
Description	Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans for 100.000 years, has a high genetic variability that motivates the study of different H. pylori populations and the diseases caused by them in order to find determinants for disease evolution. In this study we utilized both genomic and proteomic tools to compare a H. pylori strain (Nic25_A) from Nicaragua isolated from a patient with intestinal metaplasia with the P12 strain from Europe isolated from a patient with duodenal ulcer. Differences in the protein expression levels between the two strains were determined by both label-free quantification (MaxQuant) and labelling methods (tandem mass tags, TMT), utilizing a lipid-based protein immobilization (LPI™) technique to target surface protein peptides. Using the MaxQuant software, we found 52 proteins significantly differing between the two strains (up-or-down regulated by a factor of 1.5) and with TMT we were able to find 18 proteins with different expression levels between the strains. The P12 (duodenal ulcer) strain had higher expression of genes belonging to the cagPAI operon, while Nic25_A (intestinal metaplasia) had higher expression of the acid response regulator ArsR, as well as proteins regulated by ArsR; KatA, AmiE, and proteins involved in urease production. The results show that differences in protein expression can be detected by proteomic approaches in H. pylori strains of different pathogenicity, which might have implications for studies of disease progression.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:31:06.287.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carina Sihlbom
SpeciesList	scientific name: Helicobacter pylori; NCBI TaxID: 210;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-30 01:18:21	ID requested
1	2018-10-26 13:32:05	announced
⏵ 2	2024-10-22 04:31:07	announced	2024-10-22: Updated project metadata.

10.3389/fmicb.2016.01757;

Karlsson R, Thorell K, Hosseini S, Kenny D, Sihlbom C, Sj, ö, ling Å, Karlsson A, Nookaew I, Strains using Genomics and Mass Spectrometry-Based Proteomics. Front Microbiol, 7():1757(2016) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: protein expression, proteomics, TMT,Genomics, MaxQuant, Helicobacter pylori

Carina Sihlbom
contact affiliation	Proteomics Core Facility, Gothenburg University, Sweden
contact email	carina.sihlbom@gu.se
lab head
Carina Sihlbom
contact affiliation	Proteomics Core Facility / University of Gothenburg
contact email	carina.sihlbom@gu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005074
     1. Label: PRIDE project
     2. Name: Comparative Analysis of two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics