Difference between revisions of "MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry"
m (Laschp moved page Main Page to MicrobeMS - A Matlab Toolbox for Microbial Identification Based on Mass Spectrometry: New title)
Revision as of 18:22, 15 January 2020
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 7/8/8.1/10 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 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, auto-calibration and some other functions. Due to the fact that the software runs also in a complete 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 website for more information.
- 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 MALDI-TOF 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