The software package available from MicrobeMS is a program designed specifically for the analysis of MALDI-TOF mass spectra from microbial samples. The MicrobeMS software was developed by Peter Lasch at the Robert-Koch-Institut (RKI) in Berlin/Germany and can be used to identify microbial strains and species based on their mass spectral patterns. The program is a Matlab-based comprehensive package that operates under Windows 7/8/8.1. and Windows 10. 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 to a Matlab data matrix format specific to the MicrobeMS program.
The software permits standard mass spectral manipulations such as smoothing, baseline correction, normalization, peak detection, and other functions. Due to the fact that the software runs also in a complete Windows 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 website for more information.
- Specification of computer configuration
- Screenshot of MicrobeMS
- Downloading MicrobeMS
- How to install MicrobeMS
- License conditions
- How to obtain a license?
- MALDI-TOF mass spectrometry databases
- Acknowledgements, relevant publications
- Frequently asked questions (FAQ)
Preparing Mass Spectra
- Adding / editing metadata of MALDI-TOF MS data files
- Management of sample information (spectral metadata) (taxonomic information, culture conditions, sample preparation methods, etc.)
Description of the Data File Format
- 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
- 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)
- Store spectral multifiles (*.muf)
- Store peak list files (*.pkf)
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 based on neural network analysis (requires the NeuroDeveloper software package from Synthon Analytics)