Proteomics

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Reanalysis of Data-dependent acquisition based proteomic datasets of Mycobacterium avium subsp. paratuberculosis, Mycobacterium marinum and Mycobacterium vaccae

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive HF, Q Exactive

ORGANISM(S): Acyrthosiphon Pisum (pea Aphid)

SUBMITTER: Keshava Prasad T. S.  

LAB HEAD: Dr T. S. Keshava Prasad

PROVIDER: PXD045965 | 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_vaccae_GCF_001655245.1_ASM165524v1_protein.fasta Fasta
Mycobacterium_marinum_GCF_016745295.1_ASM1674529v1.fasta Fasta
PASS00954_Cytoplasm_CID_FragPipe_Search_Output.zip Other
PASS00954_Cytoplasm_HCD_PD_Search_Output.zip Other
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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]

PMID: 38358903

Publication: 1/4

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