Mycobacterium avium is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. M. avium has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of M. avium with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for Mycobacterium tuberculosis, and a genome six-frame translated database and a variant protein database of M. avium. A search of mass spectrometry data analysis against M. avium protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of M. avium proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the M. avium proteome. Thus, we present a M. avium spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.

For easy access and reproducibility of the pipeline, this dataset repository consists of final search outputs such as i) Genome alignment percentage from BWA analysis, ii) M. avium proteins annotated variants (SnpEff output), iii) Summary of annotated variants from SnpEff, iv) AutoRT model and outputs from retention time (RT) prediction analysis, v) Proteome database search results in different spectral library formats (BLIB - Skyline, DLIB - EncyclopeDIA, TSV - OpenSWATH and Spectronaut) and vi) Annotated Peptide Spectra for pseudogenes, novel gene, N-terminal extensions and variant peptides. The raw LC-MS/MS files, database search, and spectral library search results are available in the PRoteomics IDEntifications (PRIDE) repository under the ID PXD032067.