Computational protocol: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

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Protocol publication

[…] In brief, MALDI-TOF MS raw data were first converted to the open-source mzML format () by using ProteoWizard’s command-line MSConvert (). The mzML files were read into R through mzR () and custom code and processed into peak lists by using MALDIquant (). Lastly, the peak lists informed interactive data analyses and visualizations that were displayed through a default, offline internet browser with RStudio’s Shiny () package. The IDBac software is being distributed under a GNU General Public License, and links to the full code along with data acquisition and analysis tutorials can be found within . […]

Pipeline specifications

Software tools ProteoWizard, MALDIquant
Application MS-based untargeted proteomics
Organisms Bacteria, Bacillus subtilis, Hemisus marmoratus, Escherichia coli