Proteomics

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Data-dependent acquisition based proteomic analysis of Mycobacterium avium subsp. paratuberculosis ATCC 19698

ABSTRACT: Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium avium subsp. paratuberculosis is essential. Therefore, we conducted an in-depth global proteomic experiment using M. avium subsp. paratuberculosis ATCC 19698 (Map) strain followed by proteome database search and spectral library generation. The lysate was subjected to in-solution proteomic sample preparation and fractionated using an offline 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. avium subsp. paratuberculosis proteome database using Proteome Discoverer and FragPipe. The resulting peptide spectrum matches were converted into a spectral library using BiblioSpec.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mycobacterium Avium Subsp. Paratuberculosis Atcc 19698 Bacteria

SUBMITTER: Keshava Prasad T. S.  

LAB HEAD: T. S. Keshava Prasad

PROVIDER: PXD040589 | Pride | 2024-03-07

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
M_avium_para_GCF_016749935.1_ASM1674993v1_protein.fasta Fasta
M_avium_para_TP_F1_R1.raw Raw
M_avium_para_TP_F1_R2.raw Raw
M_avium_para_TP_F1_R3.raw Raw
M_avium_para_TP_F2_R1.raw Raw
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Publications

Discovery of Species-Specific Proteotypic Peptides To Establish a Spectral Library Platform for Identification of Nontuberculosis Mycobacteria from Mass Spectrometry-Based Proteomics.

Kotimoole Chinmaya Narayana CN   Ramya Vadageri Krishnamurthy VK   Kaur Parvinder P   Reiling Norbert N   Shandil Radha Krishan RK   Narayanan Shridhar S   Flo Trude Helen TH   Prasad Thottethodi Subrahmanya Keshava TSK  

Journal of proteome research 20240215 3

Nontuberculous mycobacteria are opportunistic bacteria pulmonary and extra-pulmonary infections in humans that closely resemble <i>Mycobacterium tuberculosis</i>. Although genome sequencing strategies helped determine NTMs, a common assay for the detection of coinfection by multiple NTMs with <i>M. tuberculosis</i> in the primary attempt of diagnosis is still elusive. Such a lack of efficiency leads to delayed therapy, an inappropriate choice of drugs, drug resistance, disease complications, mor  ...[more]

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