PXD032067

PXD032067 is an original dataset announced via ProteomeXchange.

Title	Novel Events, Gene Model Correction of Mycobacterium Avium by Proteogenomic Analysis
Description	Mycobacterium avium is one of the prominent disease causing bacteria in humans. It causes lymphadenitis, chronic pulmonary and extrapulmonary and disseminated infections in adults, children and immunocompromised humans. M. avium has ~4,500 predicted gene models, out of which not all are identified at proteomic level. Proteomic database search followed by proteogenomic analysis helps in the correction of gene models, identification of novel exons/genes, variant proteins. As part of this study, we performed proteomic analysis of M. avium cultures by data-dependent acquisition (DDA) and data-independent acquisition (DIA) method followed by proteogenomic analysis of M. avium proteomic data. M. avium culture was subjected to proteomic sample preparation. The resulting peptides were acquired in 120min DDA (12 bRPLC) and DIA method using EASY nLC 1200 liquid chromatogram system coupled to Orbitrap Fusion Tribrid mass spectrometer. The resulting DDA raw files were searched sequentially against the M. avium proteome database, Mycobacterium tuberculosis H37Rv and Ra proteome database (Mtb), M. avium genome six-frame translated proteome and variant proteins database, respectively. The database search result was converted into a spectral library and used for DIA data search for the validation of GSSPs and variant peptides. The database search of M. avium DDA has resulted in the identification of 2,954 M. avium proteins, 128 Mtb proteins, 174 GSSPs (M. avium genome six-frame translated proteome) and 795 SNPs corresponding to 612 proteins (variant proteins database), respectively. The M. avium proteome database search has covered 62.09% of the proteome with the identification of 2,954 proteins out of 4,757 proteins in the database. From the manual categorization of 174 GSSPs, we observed 23 N-terminal extensions, 142 pseudogene coding peptides and one each novel exon and short peptide, respectively.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:00:37.812.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032067
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Mycobacterium avium 104; NCBI TaxID: 243243;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-05 04:57:14	ID requested
1	2023-03-17 00:48:11	announced
2	2023-06-09 03:08:08	announced	2023-06-09: Updated project metadata.
⏵ 3	2023-11-14 09:00:38	announced	2023-11-14: Updated project metadata.

Kotimoole CN, Antil N, Kasaragod S, Behera SK, Aravind A, Reiling N, Flo TH, Prasad TSK, Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry-Based Proteogenomic Analysis. Mol Cell Proteomics, 22(5):100533(2023) [pubmed]

submitter keyword: DIA,Mycobacterium avium, Proteogenomics, Variant calling, DDA, LC-MS/MS

T. S. Keshava Prasad
contact affiliation	Professor and Deputy Director, Center for Systems Biology and Molecular Medicine Yenepoya Research Centre Yenepoya (Deemed to be University) University Road, Deralakatte Mangalore 575018, India
contact email	keshav@yenepoya.edu.in
lab head
Keshava Prasad T. S.
contact affiliation	Institute of Bioinformatics, Bangalore, Karnataka, India.
contact email	keshav@ibioinformatics.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD032067
     1. Label: PRIDE project
     2. Name: Novel Events, Gene Model Correction of Mycobacterium Avium by Proteogenomic Analysis