PXD045965

PXD045965 is an original dataset announced via ProteomeXchange.

Title	Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium avium subsp. paratuberculosis, Mycobacterium marinum and Mycobacterium vaccae
Description	Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium avium subsp. paratuberculosis, Mycobacterium marinum and Mycobacterium vaccae is essential. Therefore, we carried out reanalysis of publicly available M. avium subsp. paratuberculosis, M. marinum and M. vaccae proteomic dataset PXD027444, PXD003766 and PASS00954 by proteome database search and followed by spectral library generation. The raw DDA data were searched against their respective reference proteome databases using Proteome Discoverer and FragPipe. The resulting peptide spectrum matches were converted into a spectral library using BiblioSpec.
HostingRepository	PRIDE
AnnounceDate	2024-03-07
AnnouncementXML	Submission_2024-03-07_00:17:14.760.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Acyrthosiphon pisum (Pea aphid); NCBI TaxID: 7029;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-07 23:11:07	ID requested
⏵ 1	2024-03-07 00:17:18	announced

10.1021/acs.jproteome.3c00850;

Kotimoole CN, Ramya VK, Kaur P, Reiling N, Shandil RK, Narayanan S, Flo TH, Prasad TSK, Discovery of Species-Specific Proteotypic Peptides To Establish a Spectral Library Platform for Identification of Nontuberculosis Mycobacteria from Mass Spectrometry-Based Proteomics. J Proteome Res, 23(3):1102-1117(2024) [pubmed]

van Winden VJ, Ummels R, Piersma SR, Jim, é, nez CR, Korotkov KV, Bitter W, Houben EN, Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes. mBio, 7(5):(2016) [pubmed]

10.1074/mcp.m116.065813;

Kleinwort KJH, Hobmaier BF, Mayer R, H, ö, lzel C, Degroote RL, M, ä, rtlbauer E, Hauck SM, Deeg CA, Proteome Changes Profoundly in Milk. Metabolites, 11(8):(2021) [pubmed]

Zheng J, Chen L, Liu L, Li H, Liu B, Zheng D, Liu T, Dong J, Sun L, Zhu Y, Yang J, Zhang X, Jin Q, . Mol Cell Proteomics, 16(9):1578-1590(2017) [pubmed]

10.3390/metabo11080549;

10.1128/mbio.01471-16;

submitter keyword: M. marinum, M.vaccae, Proteomics, non-tuberculous mycobacteria,M. avium, LC-MS/MS

Dr 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

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/2024/03/PXD045965

PRIDE project URI

• PRIDE
  1. PXD045965
     1. Label: PRIDE project
     2. Name: Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium avium subsp. paratuberculosis, Mycobacterium marinum and Mycobacterium vaccae