PXD040615

PXD040615 is an original dataset announced via ProteomeXchange.

Title	Data-dependent acquisition based proteomic analysis of Mycobacterium abscessus ATCC 19977
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 an in-depth global proteomic experiment using M. abscessus ATCC 19977 strain followed by proteome database search and spectral library generation. The lysate was subjected for in-solution proteomic sample preparation and fractionated using an off-line C18 StageTip. Each fraction was acquired in technical triplicates using a 180 min data-dependent acquisition (DDA) method in Orbitrap Fusion Tribrid (Thermo Scientific) mass spectrometer. The resulting 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_22:20:11.793.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Keshava Prasad T. S.
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543); NCBI TaxID: 561007;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-06 04:33:39	ID requested
⏵ 1	2024-03-06 22:20:12	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]

submitter keyword: Mycobacterium abscessus, non-tuberculous mycobacteria, 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. PXD040615
     1. Label: PRIDE project
     2. Name: Data-dependent acquisition based proteomic analysis of Mycobacterium abscessus ATCC 19977