Sample Preparation for Proteomic Analysis of Neisseria meningitidis

  • Benjamin L. SchulzEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1969)


Mass spectrometry (MS) proteomics allows systematic identification, characterization, and relative quantification of the full suite of proteins in a biological sample, and is a powerful analytical approach for investigation of many aspects of the biology of Neisseria meningitidis. Here, we describe methods for robust and efficient sample preparation of the proteome of N. meningitidis suitable for diverse MS proteomics workflows.

Key words

Mass spectrometry Bottom-up proteomics Sample preparation 



This work was supported by National Health and Medical Research Council Career Development Fellowship APP1087975 to B.L.S.


  1. 1.
    Aebersold R, Mann M (2016) Mass-spectrometric exploration of proteome structure and function. Nature 537:347–355CrossRefGoogle Scholar
  2. 2.
    Gillet LC, Leitner A, Aebersold R (2016) Mass spectrometry applied to bottom-up proteomics: entering the high-throughput era for hypothesis testing. Annu Rev Anal Chem (Palo Alto, CA) 9:449–472CrossRefGoogle Scholar
  3. 3.
    Ebhardt HA, Root A, Sander C, Aebersold R (2015) Applications of targeted proteomics in systems biology and translational medicine. Proteomics 15:3193–3208CrossRefGoogle Scholar
  4. 4.
    Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R (2012) Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics 11:O111.016717CrossRefGoogle Scholar
  5. 5.
    Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R (2018) Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 14:e8126CrossRefGoogle Scholar
  6. 6.
    Lange PF, Overall CM (2013) Protein TAILS: when termini tell tales of proteolysis and function. Curr Opin Chem Biol 17:73–82CrossRefGoogle Scholar
  7. 7.
    Munk S, Refsgaard JC, Olsen JV (2016) Systems analysis for interpretation of phosphoproteomics data. Methods Mol Biol 1355:341–360CrossRefGoogle Scholar
  8. 8.
    Thaysen-Andersen M, Packer NH, Schulz BL (2016) Maturing glycoproteomics technologies provide unique structural insights into the N-glycoproteome and its regulation in health and disease. Mol Cell Proteomics 15:1773–1790CrossRefGoogle Scholar
  9. 9.
    Titeca K, Lemmens I, Tavernier J, Eyckerman S (2019) Discovering cellular protein-protein interactions: technological strategies and opportunities. Mass Spectrom Rev 38:79–111CrossRefGoogle Scholar
  10. 10.
    Christodoulides M (2014) Neisseria proteomics for antigen discovery and vaccine development. Expert Rev Proteomics 11:573–591CrossRefGoogle Scholar
  11. 11.
    Christodoulides M, Heckels J (2017) Novel approaches to Neisseria meningitidis vaccine design. Pathog Dis 75:ftx033CrossRefGoogle Scholar
  12. 12.
    Rinaudo CD, Telford JL, Rappuoli R, Seib KL (2009) Vaccinology in the genome era. J Clin Invest 119:2515–2525CrossRefGoogle Scholar
  13. 13.
    Tsolakos N, Brookes C, Taylor S, Gorringe A, Tang CM, Feavers IM, Wheeler JX (2014) Identification of vaccine antigens using integrated proteomic analyses of surface immunogens from serogroup B Neisseria meningitidis. J Proteome 101:63–76Google Scholar
  14. 14.
    van Alen T, Claus H, Zahedi RP, Groh J, Blazyca H, Lappann M, Sickmann A, Vogel U (2010) Comparative proteomic analysis of biofilm and planktonic cells of Neisseria meningitidis. Proteomics 10:4512–4521Google Scholar
  15. 15.
    Peak IR, Chen A, Jen FE, Jennings C, Schulz BL, Saunders NJ, Kahn A, Seifert HS, Jennings MP (2016) Neisseria meningitidis lacking the major porins PorA and PorB are viable and modulate apoptosis and the oxidative burst of neutrophils. J Proteome Res 15:2356–2365Google Scholar
  16. 16.
    Bernardini G, Laschi M, Serchi T, Arena S, D’Ambrosio C, Braconi D, Scaloni A, Santucci A (2011) Mapping phosphoproteins in Neisseria meningitidis serogroup A. Proteomics 11:1351–1358Google Scholar
  17. 17.
    Jen FE, Warren MJ, Schulz BL, Power PM, Swords WE, Weiser JN, Apicella MA, Edwards JL, Jennings MP (2013) Dual pili post-translational modifications synergize to mediate meningococcal adherence to platelet activating factor receptor on human airway cells. PLoS Pathog 9:e1003377CrossRefGoogle Scholar
  18. 18.
    Chamot-Rooke J, Rousseau B, Lanternier F, Mikaty G, Mairey E, Malosse C, Bouchoux G, Pelicic V, Camoin L, Nassiff X, Dumenil G (2007) Alternative Neisseria spp. type IV pilin glycosylation with a glyceramido acetamido trideoxyhexose residue. Proc Natl Acad Sci U S A 104:14783–14788Google Scholar
  19. 19.
    Ku SC, Schulz BL, Power PM, Jennings MP (2009) The pilin O-glycosylation pathway of pathogenic Neisseria is a general system that glycosylates AniA, an outer membrane nitrite reductase. Biochem Biophys Res Commun 378:84–89Google Scholar
  20. 20.
    Schulz BL, Jen FE, Power PM, Jones CE, Fox KL, Ku SC, Blanchfield JT, Jennings MP (2013) Identification of bacterial protein O-oligosaccharyltransferases and their glycoprotein substrates. PLoS One 8:e62768CrossRefGoogle Scholar
  21. 21.
    Gault J, Malosse C, Dumenil G, Chamot-Rooke J (2013) A combined mass spectrometry strategy for complete posttranslational modification mapping of Neisseria meningitidis major pilin. J Mass Spectrom 48:1199–1206Google Scholar
  22. 22.
    Gault J, Malosse C, Machata S, Millien C, Podglajen I, Ploy MC, Costello CE, Dumenil G, Chamot-Rooke J (2014) Complete posttranslational modification mapping of pathogenic Neisseria meningitidis pilins requires top-down mass spectrometry. Proteomics 14:1141–1151Google Scholar
  23. 23.
    Müller T, Winter D (2017) Systematic evaluation of protein reduction and alkylation reveals massive unspecific side effects by iodine-containing reagents. Mol Cell Proteomics 16:1173–1187CrossRefGoogle Scholar
  24. 24.
    Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362CrossRefGoogle Scholar
  25. 25.
    Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J (2014) Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 10:757CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneAustralia
  2. 2.Australian Infectious Diseases Research CentreThe University of QueenslandBrisbaneAustralia

Personalised recommendations