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PXD011364

PXD011364 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComparative proteomics of Helicobacter pylori strains reveals geographical features rather than genomic variations
DescriptionHelicobacter pylori, which is known as pathogens of various gastric diseases, have many types of genome sequence variants. That is part of the reason why pathogenesis and infection mechanisms of the H. pylori-driven gastric diseases have not been well clarified yet. Here we performed a large-scale proteome analysis to profile the heterogeneity of the proteome expression of 7 H. pylori strains by using LC/MS/MS-based proteomics approach combined with a customized database consisting of non-redundant tryptic peptide sequences derived from full genome sequences of 52 H. pylori strains. The non-redundant peptide database enabled us to identify more peptides in the database search of MS/MS data, compared with a simply merged protein database. Using the approach we performed proteome analysis of genome-unknown strains of H. pylori in as large-scale as genome-known ones. Clustering of the H. pylori strains using the proteome profiling slightly differed from the genome profiling and more clearly divided the strains into two groups based on the isolated area. Furthermore, we also identified phosphorylated proteins and sites of the H. pylori strains and obtained phosphorylation motif located in the N-terminus, which are commonly observed in bacteria.
HostingRepositoryjPOST
AnnounceDate2018-12-28
AnnouncementXMLSubmission_2022-09-18_03:43:45.685.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNaoyuki Sugiyama
SpeciesList scientific name: Helicobacter pylori F16; NCBI TaxID: 866344; scientific name: Helicobacter pylori F30; NCBI TaxID: 866345; scientific name: Helicobacter pylori F32; NCBI TaxID: 102608; scientific name: Helicobacter pylori OK113; NCBI TaxID: 1248725; scientific name: Helicobacter pylori OK310; NCBI TaxID: 1248726; scientific name: Helicobacter pylori; NCBI TaxID: 210;
ModificationListS-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine
InstrumentQ Exactive; TripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-10-15 21:52:17ID requested
12018-12-27 16:26:02announced
22021-02-04 17:23:58announced2021-02-04: Updated FTP location.
32022-09-18 03:43:46announced2022-09-18: Updated FTP location.
Publication List
Sugiyama N, Miyake S, Lin MH, Wakabayashi M, Marusawa H, Nishiumi S, Yoshida M, Ishihama Y, Comparative proteomics of Helicobacter pylori strains reveals geographical features rather than genomic variations. Genes Cells, 24(2):139-150(2019) [pubmed]
Keyword List
submitter keyword: Helicobacter pylori, whole proteome
Contact List
Yasushi Ishihama
lab head
Naoyuki Sugiyama
contact affiliationKyoto University
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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