Abstract
The use of proteomic technologies to characterize and study the proteome of mycobacteria has provided important information in terms of function, diversity, protein–protein interactions, and host-pathogen interactions in Mycobacterium spp. There are many different mass spectrometry methodologies that can be applied to proteomics studies of mycobacteria and microorganisms in general. Sample processing and appropriate study design are critical to generating high-quality data regardless of the mass spectrometry method applied. Appropriate study design relies on statistical rigor and data curation using bioinformatics approaches that are widely applicable regardless of the organism or system studied. Sample processing, on the other hand, is often a niched process specific to the physiology of the organism or system under investigation. Therefore, in this chapter, we will provide protocols for processing mycobacterial protein samples for the specific application of Top-down and Bottom-up proteomic analyses.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM (2017) Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol 13(3):922. https://doi.org/10.15252/msb.20167062
Albeldas C, Ganief N, Calder B, Nakedi KC, Garnett S, Nel AJM, Blackburn JM, Soares NC (2018) Global proteome and phosphoproteome dynamics indicate novel mechanisms of vitamin C induced dormancy in mycobacterium smegmatis. J Proteome 180:1–10. https://doi.org/10.1016/j.jprot.2017.10.006
Hoffmann E, Machelart A, Song OR, Brodin P (2018) Proteomics of mycobacterium infection: moving towards a better understanding of pathogen-driven immunomodulation. Front Immunol 9:86. https://doi.org/10.3389/fimmu.2018.00086
Parra J, Marcoux J, Poncin I, Canaan S, Herrmann JL, Nigou J, Burlet-Schiltz O, Riviere M (2017) Scrutiny of Mycobacterium tuberculosis 19 kDa antigen proteoforms provides new insights in the lipoglycoprotein biogenesis paradigm. Sci Rep 7:43682. https://doi.org/10.1038/srep43682
Kruh-Garcia NA, Wolfe LM, Chaisson LH, Worodria WO, Nahid P, Schorey JS, Davis JL, Dobos KM (2014) Detection of Mycobacterium tuberculosis peptides in the exosomes of patients with active and latent M. tuberculosis infection using MRM-MS. PLoS One 9(7):e103811. https://doi.org/10.1371/journal.pone.0103811
Kruh-Garcia NA, Wolfe LM, Dobos KM (2015) Deciphering the role of exosomes in tuberculosis. Tuberculosis (Edinb) 95(1):26–30. https://doi.org/10.1016/j.tube.2014.10.010
Mehaffy C, Dobos KM, Nahid P, Kruh-Garcia NA (2017) Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum. Clin Proteomics 14:21. https://doi.org/10.1186/s12014-017-9156-y
Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin Z, Lippens JL, Aluri KC, Sarin R, Chen B, Lantz C, Jung W, Johnson KR, Koller A, Wolff JJ, Campuzano IDG, Auclair JR, Ivanov AR, Whitelegge JP, Pasa-Tolic L, Chamot-Rooke J, Danis PO, Smith LM, Tsybin YO, Loo JA, Ge Y, Kelleher NL, Agar JN (2019) Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nat Methods 16(7):587–594. https://doi.org/10.1038/s41592-019-0457-0
Binz PA, Barkovich R, Beavis RC, Creasy D, Horn DM, Julian RK Jr, Seymour SL, Taylor CF, Vandenbrouck Y (2008) Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol 26(8):862. https://doi.org/10.1038/nbt0808-862
Martinez-Bartolome S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernaez ML, Gutierrez-Blazquez MD, Velarde LF, Aloria K, Beaskoetxea J, Medina-Aunon JA, Albar JP (2013) Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. J Proteome 95:84–88. https://doi.org/10.1016/j.jprot.2013.02.026
Taylor CF (2006) Minimum reporting requirements for proteomics: a MIAPE primer. Proteomics 6(Suppl 2):39–44. https://doi.org/10.1002/pmic.200600549
Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Huhmer A, Kussmann M, Lilley K, Macht M, Mann M, Muller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK Jr (2008) Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol 26(8):860–861. https://doi.org/10.1038/nbt0808-860
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25(8):887–893. https://doi.org/10.1038/nbt1329
Bisson GP, Mehaffy C, Broeckling C, Prenni J, Rifat D, Lun DS, Burgos M, Weissman D, Karakousis PC, Dobos K (2012) Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis. J Bacteriol 194(23):6441–6452. https://doi.org/10.1128/JB.01013-12
Nieto Ramirez LM, Mehaffy C, Dobos KM (2019) Protein profile of different cellular fractions from Mycobacterium tuberculosis strains after exposure to isoniazid. Data Brief 24:103953. https://doi.org/10.1016/j.dib.2019.103953
Nieto RL, Mehaffy C, Dobos KM (2016) Comparing isogenic strains of Beijing genotype Mycobacterium tuberculosis after acquisition of isoniazid resistance: a proteomics approach. Proteomics 16(9):1376–1380. https://doi.org/10.1002/pmic.201500403
Nieto RL, Mehaffy C, Islam MN, Fitzgerald B, Belisle J, Prenni J, Dobos K (2018) Biochemical characterization of isoniazid-resistant Mycobacterium tuberculosis: can the analysis of clonal strains reveal novel targetable pathways? Mol Cell Proteomics 17(9):1685–1701. https://doi.org/10.1074/mcp.RA118.000821
Duncan C, Jamieson FB, Troudt J, Izzo L, Bielefeldt-Ohmann H, Izzo A, Mehaffy C (2017) Whole transcriptomic and proteomic analyses of an isogenic M. tuberculosis clinical strain with a naturally occurring 15 kb genomic deletion. PLoS One 12(6):e0179996. https://doi.org/10.1371/journal.pone.0179996
Mehaffy C, Hess A, Prenni JE, Mathema B, Kreiswirth B, Dobos KM (2010) Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis. Proteomics 10:1966–1984. https://doi.org/10.1002/pmic.200900836
Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, MacCoss MJ (2016) An automated pipeline to monitor system performance in liquid chromatography-tandem mass spectrometry proteomic experiments. J Proteome Res 15(12):4763–4769. https://doi.org/10.1021/acs.jproteome.6b00744
Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ (2014) Implementation of statistical process control for proteomic experiments via LC MS/MS. J Am Soc Mass Spectrom 25(4):581–587. https://doi.org/10.1007/s13361-013-0824-5
Bielow C, Mastrobuoni G, Kempa S (2016) Proteomics quality control: quality control software for MaxQuant results. J Proteome Res 15(3):777–787. https://doi.org/10.1021/acs.jproteome.5b00780
Dogu E, Mohammad-Taheri S, Abbatiello SE, Bereman MS, MacLean B, Schilling B, Vitek O (2017) MSstatsQC: longitudinal system suitability monitoring and quality control for targeted proteomic experiments. Mol Cell Proteomics 16(7):1335–1347. https://doi.org/10.1074/mcp.M116.064774
Taverner T, Karpievitch YV, Polpitiya AD, Brown JN, Dabney AR, Anderson GA, Smith RD (2012) DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinformatics 28(18):2404–2406. https://doi.org/10.1093/bioinformatics/bts449
Bourmaud A, Gallien S, Domon B (2015) A quality control of proteomic experiments based on multiple isotopologous internal standards. EuPA Open Proteom 8:16–21. https://doi.org/10.1016/j.euprot.2015.07.010
Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA (2015) Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 15(5–6):930–949. https://doi.org/10.1002/pmic.201400302
Riffle M, Eng JK (2009) Proteomics data repositories. Proteomics 9(20):4653–4663. https://doi.org/10.1002/pmic.200900216
Demeure K, Quinton L, Gabelica V, De Pauw E (2007) Rational selection of the optimum MALDI matrix for top-down proteomics by in-source decay. Anal Chem 79(22):8678–8685. https://doi.org/10.1021/ac070849z
Guray MZ, Zheng S, Doucette AA (2017) Mass spectrometry of intact proteins reveals +98 u chemical artifacts following precipitation in acetone. J Proteome Res 16(2):889–897. https://doi.org/10.1021/acs.jproteome.6b00841
Link AJ, LaBaer J (2011) Trichloroacetic acid (TCA) precipitation of proteins. Cold Spring Harb Protoc 2011(8):993–994. https://doi.org/10.1101/pdb.prot5651
Doucette AA, Vieira DB, Orton DJ, Wall MJ (2014) Resolubilization of precipitated intact membrane proteins with cold formic acid for analysis by mass spectrometry. J Proteome Res 13(12):6001–6012. https://doi.org/10.1021/pr500864a
Wessel D, Flugge UI (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 138(1):141–143. https://doi.org/10.1016/0003-2697(84)90782-6
Acknowledgement
This work was supported by ATCC contract 2010-0516-0005 (a subcontract of NIH-NIAID Contract HHSN272201000027c) and ATCC contract 2016-0550-0002 (a subcontract of NIH-NIAID contract HHSN272201600013c.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Mehaffy, C., Lucas, M., Kruh-Garcia, N.A., Dobos, K.M. (2021). Methods for Proteomic Analyses of Mycobacteria. In: Parish, T., Kumar, A. (eds) Mycobacteria Protocols. Methods in Molecular Biology, vol 2314. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1460-0_23
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1460-0_23
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1459-4
Online ISBN: 978-1-0716-1460-0
eBook Packages: Springer Protocols