PXD046063

PXD046063 is an original dataset announced via ProteomeXchange.

Title	Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium smegmatis
Description	Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium smegmatis is essential. Therefore, we carried out reanalysis of publicly available M. smegmatis proteomic dataset PXD003303, PXD004197, PXD010020, PXD016241, PXD017602, PXD027848, PXD027855 and PXD029588 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_00:27:48.762.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Mycobacterium smegmatis; NCBI TaxID: 1772;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-11 06:52:36	ID requested
⏵ 1	2024-03-07 00:27:54	announced

Ganief N, Sjouerman J, Albeldas C, Nakedi KC, Hermann C, Calder B, Blackburn JM, Soares NC, and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage. Emerg Microbes Infect, 7(1):212(2018) [pubmed]

Hillion M, Bernhardt J, Busche T, Rossius M, Maa, ß S, Becher D, Rawat M, Wirtz M, Hell R, R, ü, ckert C, Kalinowski J, Antelmann H, Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress. Sci Rep, 7(1):1195(2017) [pubmed]

Thouvenel L, Prevot G, Chiaradia L, Parra J, Mouton-Barbosa E, Locard-Paulet M, Marcoux J, Tropis M, Burlet-Schiltz O, Daff, é M, Guilhot C, Etienne G, Chalut C, The final assembly of trehalose polyphleates takes place within the outer layer of the mycobacterial cell envelope. J Biol Chem, 295(32):11184-11194(2020) [pubmed]

Giddey AD, de Kock E, Nakedi KC, Garnett S, Nel AJ, Soares NC, Blackburn JM, A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations. Sci Rep, 7():43858(2017) [pubmed]

10.1038/s41426-018-0210-2;

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]

10.3389/fmed.2021.723667;

10.3389/fmicb.2022.811774;

Giddey AD, Ganief TA, Ganief N, Koch A, Warner DF, Soares NC, Blackburn JM, to Subinhibitory Rifampicin Exposure. Front Med (Lausanne), 8():723667(2021) [pubmed]

10.1074/jbc.ra120.013299;

Kriel NL, Heunis T, Sampson SL, Gey van Pittius NC, Williams MJ, Warren RM, Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. BMC Mol Cell Biol, 21(1):19(2020) [pubmed]

10.1038/srep43858;

Dow A, Burger A, Marcantonio E, Prisic S, . Front Microbiol, 13():811774(2022) [pubmed]

10.1038/s41598-017-01179-4;

10.1186/s12860-020-00261-6;

submitter keyword: M. smegmatis, Proteomics, non-tuberculous mycobacteria, LC-MS/MS

Dr T.
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/PXD046063

PRIDE project URI

• PRIDE
  1. PXD046063
     1. Label: PRIDE project
     2. Name: Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium smegmatis