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).
See also the MicrobeMS web site for more information.
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