PXD006787

PXD006787 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Proteogenomic study of Clavibacter michiganensis subsp. michiganensis strain NCPPB382
Description	Clavibacter michiganensis subsp. michiganensis is an important Gram-positive phytopathogenic bacteria that causes bacterial wilt and canker in tomato. The genome of the type strain, NCPPB382, has been sequenced and annotated, however comparative genomics suggests that certain regions are under- or misannotated. In order to improve the genome annotation, we have undertaken a proteogenomic study of this important pathogen. Samples were grown in culture and the proteome of the pellet and supernatant were analyzed separately using shotgun HPLC-MS/MS. These proteomics datasets were analyzed and a number of missing gene were found and a number of existing gene calls were modified.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:51:23.157.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paul Stodghill
SpeciesList	scientific name: Clavibacter michiganensis subsp. michiganensis NCPPB 382; NCBI TaxID: 443906;
ModificationList	methylthiolated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-23 01:36:14	ID requested
1	2019-01-31 04:21:32	announced
⏵ 2	2024-10-22 04:51:31	announced	2024-10-22: Updated project metadata.

Publication List

10.1002/pmic.201800224;
Peritore-Galve FC, Schneider DJ, Yang Y, Thannhauser TW, Smart CD, Stodghill P, Proteome Profile and Genome Refinement of the Tomato-Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis. Proteomics, 19(7):e1800224(2019) [pubmed]

10.1002/pmic.201800224;

Peritore-Galve FC, Schneider DJ, Yang Y, Thannhauser TW, Smart CD, Stodghill P, Proteome Profile and Genome Refinement of the Tomato-Pathogenic Bacterium Clavibacter michiganensis subsp. michiganensis. Proteomics, 19(7):e1800224(2019) [pubmed]

Keyword List

submitter keyword: HPLC-MSMS,Proteogenomics, Clavibacter michiganensis subsp. michiganensis

submitter keyword: HPLC-MSMS,Proteogenomics, Clavibacter michiganensis subsp. michiganensis

Contact List

Paul Stodghill
contact affiliation	Emerging Pests and Pathogens Researh Unit Robert W. Holley Center, USDA-ARS-NEA 538 Tower Road, Ithaca, NY 14853
contact email	paul.stodghill@ars.usda.gov
lab head
Paul Stodghill
contact affiliation	USDA-ARS
contact email	paul.stodghill@ars.usda.gov
dataset submitter

Full Dataset Link List

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/2019/01/PXD006787
PRIDE project URI

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/2019/01/PXD006787

PRIDE project URI

Repository Record List

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