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Shotgun Proteomics pp 191–201Cite as

Proteogenomic Approach for Mycobacterium tuberculosis Investigation

Part of the Methods in Molecular Biology book series (MIMB,volume 2259)

Abstract

Recent advances in MS/MS technology have made it possible to use proteomic data to predict protein-coding sequences. This approach is called proteogenomics, and it allows to correctly translate start and stop sites and to reveal new open reading frames. Here, we focus on using proteogenomics to improve the annotation of Mycobacteriumtuberculosis strains. We also describe detail procedures of the extraction of proteins and their further preparation for LC–MS/MS analysis and outline the main steps of data analysis.

Key words

  • Proteome
  • Beijing B0/W148
  • Proteomic
  • Label-free
  • Genome

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References

  1. Målen H, De Souza GA, Pathak S, Søfteland T, Wiker HG (2011) Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol 11:18

    CrossRef  Google Scholar 

  2. Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK et al (2013) The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis. Cell Host Microbe 13(5):602–612

    CAS  CrossRef  Google Scholar 

  3. Xiong Y, Chalmers MJ, Gao FP, Cross TA, Marshall AG (2005) Identification of Mycobacterium tuberculosis H37Rv integral membrane proteins by one-dimensional gel electrophoresis and liquid chromatography electrospray ionization tandem mass spectrometry. J Proteome Res 4(3):855–861

    CAS  CrossRef  Google Scholar 

  4. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D et al (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393(6685):537–544

    CAS  CrossRef  Google Scholar 

  5. Camus JC, Pryor MJ, Médigue C, Cole ST (2002) Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148(10):2967–2973

    CAS  CrossRef  Google Scholar 

  6. de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG (2008) High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics 9:316

    CrossRef  Google Scholar 

  7. Heunis T, Dippenaar A, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC et al (2017) Proteogenomic investigation of strain variation in clinical Mycobacterium tuberculosis isolates. J Proteome Res 16(10):3841–3851

    CAS  CrossRef  Google Scholar 

  8. Bespyatykh JA, Shitikov EA, Ilina EN (2017) Proteomics for the investigation of mycobacteria. Acta Nat 9(1):15–25

    CAS  CrossRef  Google Scholar 

  9. Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK et al (2011) Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 10(12):111.011627

    CrossRef  Google Scholar 

  10. Shitikov E, Kolchenko S, Mokrousov I, Bespyatykh J, Ischenko D, Ilina E, Govorun V (2017) Evolutionary pathway analysis and unified classification of east Asian lineage of Mycobacterium tuberculosis. Sci Rep 7(1):9227

    CrossRef  Google Scholar 

  11. Bespyatykh J, Smolyakov A, Guliaev A, Shitikov E, Arapidi G, Butenko I et al (2019) Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains. J Proteome 192:18–26

    CAS  CrossRef  Google Scholar 

  12. Bespyatykh J, Shitikov E, Guliaev A, Smolyakov A, Klimina K, Veselovsky V et al (2019) System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 9:19255

    CAS  CrossRef  Google Scholar 

  13. Bespyatykh J, Smolyakov AV, Arapidi GP, Shitikov EA (2019) Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster. J Integr OMICS 9(2):1–81

    Google Scholar 

  14. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    CAS  CrossRef  Google Scholar 

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Author information

Authors and Affiliations

  1. Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia

    Julia Bespyatykh, Georgij Arapidi & Egor Shitikov

Authors
  1. Julia Bespyatykh
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  2. Georgij Arapidi
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  3. Egor Shitikov
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Editor information

Editors and Affiliations

  1. Department of Food Technology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain

    Mónica Carrera

  2. Department of Food Technology, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Vigo, Spain

    Jesús Mateos

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Bespyatykh, J., Arapidi, G., Shitikov, E. (2021). Proteogenomic Approach for Mycobacterium tuberculosis Investigation. In: Carrera, M., Mateos, J. (eds) Shotgun Proteomics. Methods in Molecular Biology, vol 2259. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1178-4_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1178-4_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1177-7

  • Online ISBN: 978-1-0716-1178-4

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