PXD045930

PXD045930 is an original dataset announced via ProteomeXchange.

Title	Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium abscessus
Description	Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium abscessus is essential. Therefore, we carried out reanalysis of publicly available M. abscessus proteomic dataset MSV000085363, PXD015680 and PXD022644 by proteome database search and followed by spectral library generation. The raw DDA data were searched against the M. abscessus proteome database 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_2024-03-06_22:45:21.887.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543); NCBI TaxID: 561007;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-06 07:53:51	ID requested
⏵ 1	2024-03-06 22:45:27	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]

Rojony R, Danelishvili L, Campeau A, Wozniak JM, Gonzalez DJ, Bermudez LE, to Environmental Stress and Clinically Used Antibiotics Reveals Common Proteome Response among Pathogenic Mycobacteria. Microorganisms, 8(5):(2020) [pubmed]

10.3390/microorganisms8050698;

10.1371/journal.pone.0238178;

10.1128/aac.01956-20;

Sayed ARM, Shah NR, Basso KB, Kamat M, Jiao Y, Moya B, Sutaria DS, Lang Y, Tao X, Liu W, Shin E, Zhou J, Werkman C, Louie A, Drusano GL, Bulitta JB, -Lactamase Inhibitors in Mycobacterium abscessus. Antimicrob Agents Chemother, 65(1):(2020) [pubmed]

Madani A, Mallick I, Guy A, Crauste C, Durand T, Fourquet P, Audebert S, Camoin L, Canaan S, Cavalier JF, Dissecting the antibacterial activity of oxadiazolone-core derivatives against Mycobacterium abscessus. PLoS One, 15(9):e0238178(2020) [pubmed]

submitter keyword: M. abscessus, Proteomics, non-tuberculous mycobacteria, 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/PXD045930

PRIDE project URI

• PRIDE
  1. PXD045930
     1. Label: PRIDE project
     2. Name: Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium abscessus