MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry

Introduction

The MicrobeMS software package is a program specifically designed for the analysis of MALDI-TOF mass spectra of microbial samples. The MicrobeMS software was developed by Peter Lasch at the Robert-Koch-Institute (RKI) in Berlin/Germany and can be used to identify microbial strains and species based on their mass spectral patterns. The program is a comprehensive Matlab-based package that operates under Windows 7/8/8.1/10/11 and LINUX (Debian, MicrobeMS versions later than 0.81). Original MALDI-TOF mass spectra in the format defined by Bruker Daltonics or by Shimadzu (via the mzXML data format) can be imported, processed and converted into a Matlab data matrix format specific to the MicrobeMS program.

The software allows standard mass spectrometry manipulations such as smoothing, baseline correction, normalization, peak detection, auto-calibration and some other functions. Since the software also runs in a full Windows or LINUX 64-bit environment, the number of spectra in the data sets is limited only by the amount of available memory (RAM).

Getting Started

• Specification of computer configuration
• Screenshot of MicrobeMS
• Downloading MicrobeMS
• How to install MicrobeMS
• License conditions
• How to obtain a license?
• Mass spectrometry databases
• Acknowledgements, relevant publications
• Frequently asked questions (FAQ)

Preparing Mass Spectra

• Adding / editing metadata of MS data files
• Management of sample information (spectral metadata) (taxonomic information, culture conditions, sample preparation methods, etc.)

Description of the Data File Formats

• Description of the format of spectral multifiles (*.muf)
• Description of the format of peak list files (*.pkf)
• Description of the parameter file 'microbems.opt'

Import and Export of Mass Spectra and Mass Spectral Libraries

• Load spectral data files acquired by using Bruker's mass spectrometers
• Load / store spectral multifiles (*.muf)
• Load / store peak list files (*.pkf)
• Store spectra in a Bruker-specific data format
• Store spectra in a standard ASCII data format (export to ASCII)
• Store peaklist data in a format specific to the NeuroDeveloper software (export to NeuroDeveloper)
• Import mass spectral data from mzXML data (allows importing spectra from Shimadzu/bioMérieux systems)

Spectral Analysis and Visualization

• Spectral pre-processing: smoothing, baseline correction, normalization, cut, auto-calibration, data reduction
• Peak detection
• Averaging mass spectra
• Class assignment
• Display spectral metadata
• The log-file (logfile.txt)

Identification and Classification

• Unsupervised hierarchical cluster analysis
• Creating database spectra from individual microbial mass spectra
• Compiling mass spectral databases
• Microbial identification based on mass spectral libraries and interspectral distances
• Identification analysis by artificial neural networks (ANN, requires the NeuroDeveloper software package from Synthon Analytics)
• Identification analysis by means of LC-MS¹ and in silico databases

Identification of MS Biomarker Peaks

• Generation of pseudo-gel views from microbial mass spectra
• Peak frequency tests
• Two-samples t-tests
• Wilcoxon rank-sum tests