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 software was developed by Peter Lasch at the Robert-Koch-Institute (RKI) in Berlin/Germany and can be used to identify microbial 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 to mention some preprocessing functions. Furthermore, functionalities of the software include, among others, microbial identification analysis based on spectral distances and machine learning methods (ML), e.g. by artificial neural networks (ANN) with visualization of the identification results, unsupervised hierarchical cluster analysis, biomarker analysis, pseudo-gel view generation, as well as microbial mass spectra database management including interfaces for organizing mass spectral metadata. 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

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

Management of Metadata Information

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

Description of Data File Formats Specific to MicrobeMS

• Description of the format of spectral multifiles (*.muf)
• Description of the format of peak list files (*.pkf)
• Description of the format of quality test files (*.mat)
• 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
• Quality tests of MALDI-ToF mass spectra
• Peak detection
• Averaging mass spectra
• 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
• How to perform class assignments?
• Peak frequency tests
• Two-samples t-tests
• Wilcoxon rank-sum tests