PXD009489

PXD009489 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains
Description	Nowadays proteomics is the one of the major instruments for editing and correct decryption of genomic information. Genomic correction of socially significant pathogens, like Mycobacterium tuberculosis, is by far the most relevant. We conducted proteogenomic analysis of W-148 strain, which belong to the Beijing B0/W148 cluster. Strains of this cluster possess unique pathogenic properties and have a unique genome organization. Taking into account a high similarity of cluster strains at the genomic level we analysed MS/MS datasets obtained for 63 clinical isolates of Beijing B0/W148. Based on H37Rv and W-148 annotations we identified 2,546 proteins, representing more than 60 % of total proteome. A set of peptides (n=404), specific for W-148 was found in comparison with H37Rv. Start sites for 32 genes were corrected based on combination of LC-MS/MS proteomic data with genomic six frame translation. Additionally, presence of peptides for 10 pseudogenes has been confirmed. Thus, the data obtained by us undoubtedly shows the need for conducting genome annotation based on proteomic data. Corrected during the study W-148 genome annotation will allow to use it in studies on Beijing B0/W148 cluster strains.
HostingRepository	PRIDE
AnnounceDate	2018-10-08
AnnouncementXML	Submission_2018-10-08_11:08:30.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD009489
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Smolyakov
SpeciesList	scientific name: Mycobacterium tuberculosis; NCBI TaxID: 1773;
ModificationList	Ammonia-loss; Dehydrated; Oxidation; Acetyl; Carbamidomethyl
Instrument	Q Exactive HF; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-13 01:20:34	ID requested
⏵ 1	2018-10-08 11:08:31	announced

Bespyatykh J, Smolyakov A, Guliaev A, Shitikov E, Arapidi G, Butenko I, Dogonadze M, Manicheva O, Ilina E, Zgoda V, Govorun V, Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains. J Proteomics, 192():18-26(2019) [pubmed]

curator keyword: Biological

submitter keyword: Mycobacterium tuberculosis, Beijing B0/W148, proteomics, proteogenomics, Label-free proteomic analysis

Egor Shitikov
contact affiliation	PhD, Head of laboratory of Molecular microbial genetics Federal Research and Clinical Centre of Physical-Chemical Medicine
contact email	eshitikov@mail.ru
lab head
Alexander Smolyakov
contact affiliation	Moscow Institute of Physics and Technology
contact email	sashasmolykov@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009489
     1. Label: PRIDE project
     2. Name: Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains