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A new data processing routine facilitating the identification of surface adhered proteins from bacterial conditioning films via QCM-D/MALDI-ToF/MS

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Abstract

Conditioning films are an important factor in the initiation and development of microbial biofilms, which are the leading cause of chronic infections associated with medical devices. Here, we analyzed the protein content of conditioning films formed after exposure to supernatants of cultures of the human pathogen Pseudomonas aeruginosa PAO1. Adhesion of substances from the supernatant was monitored using quartz crystal microbalance with dissipation monitoring (QCM-D) sensor chips modified with the commonly used implant material titanium dioxide (TiO2). Attached proteins were identified after on-chip digestion using matrix-assisted laser desorption/ionization (MALDI) time of flight (ToF) mass spectrometry (MS), and a new data processing tool consisting of an XML-database with theoretical tryptic peptides of every PAO1 protein and PHP scripts. Sub-databases containing only proteins, that we found in all replicates, were created and used for MS/MS precursor selection. The obtained MS/MS peaklists were then matched against theoretical fragmentations of the expected peptide sequences to verify protein identification. Using this approach we were able to identify 40 surface-associated proteins. In addition to extracellular proteins such as adhesins, a number of intra-cellular proteins were identified which may be involved in conditioning film formation, suggesting an as-yet unidentified role for these proteins, possibly after cell lysis.

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Acknowledgements

This work was funded by the Helmholtz Programme BioInterfaces in Technology and Medicine (BIFTM) of the Karlsruhe Institute of Technology (KIT).

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Authors and Affiliations

  1. Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany

    Siegfried Hohmann, Anke Neidig, Boris Kühl, Frank Kirschhöfer & Gerald Brenner-Weiß

  2. Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada

    Jörg Overhage

Authors
  1. Siegfried Hohmann
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  2. Anke Neidig
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  3. Boris Kühl
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Correspondence to Siegfried Hohmann.

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Hohmann, S., Neidig, A., Kühl, B. et al. A new data processing routine facilitating the identification of surface adhered proteins from bacterial conditioning films via QCM-D/MALDI-ToF/MS. Anal Bioanal Chem 409, 5965–5974 (2017). https://doi.org/10.1007/s00216-017-0521-5

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  • DOI: https://doi.org/10.1007/s00216-017-0521-5

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