Frequently Asked Questions (FAQ)
What is MicrobeMS?
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.
What is M.A.R.A.-MS and why M.A.R.A.-MS has been renamed?
MicrobeMS was originally named after Peter Lasch's daughter Mara (M.A.R.A.-MS - software for Microbial ARchive Analysis), which was not a good idea at all, see this link. Although the web pages have been already revised for the most part, the old name is still used in some instances (this wiki, domain name, etc.).
What is the most actual version of MicrobeMS?
The most actual version of the MicrobeMS software is MicrobeMS v0.80 from February 2017. The software can be downloaded here.
New functions of version 0.80 (selection):
- Re-designed interface to Artificial Neural Networks
- The import filter for binary Bruker Daltonics spectra files has been completely revised. This filter supports now also importing of MS data calibrated with the function cubic enhanced.
- New design of the function Microbial identification based on mass spectral libraries and interspectral distances: Matlab code for calculation of inter-spectral distances is now fully vectorized => speed improvement by a factor of ~4.
- Enhanced functionality of the option vary calibration parameters
- and many code improvements & bugfixes.
Please refer to the MicrobeMS website for more information.
I have installed MicrobeMS, but I would like to use also spectral databases
Databases of microbial mass spectra are not shipped with the software (except some test spectra from selected strains of Escherichia coli). For a limited number of users we provide on personal request spectral databases from our Yersinia and Bacillus study (signing of a data transfer agreement - DTA - will be required). Please send an e-mail with your request to the following address: email@example.com
UPDATE OCT 2016: Since October 27, 2016 the database from the Robert Koch Institute (RKI) with MALDI-TOF mass spectra from the genera Bacillus, Yersinia and Burkholderia is available for download (Zenodo, Creatives Commons license, CC-BY-NC-SA). The RKI database currently comprises 5531 spectra in the Bruker data format and the respective peak list file (*.pkf data format) allowing microbial identification using MicrobeMS version 0.80 and later, see the publication A MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch Institute (RKI).
UPDATE MAY 2017: The second version of the RKI MALDI-TOF MS database is available (Creatives Commons license, CC-BY-NC-SA), see http://doi.org/10.5281/zenodo.582602 for details.
Is there a stand-alone version of MicrobeMS available
Yes, since November 2016 a stand-alone version of the MicrobeMS toolbox is available. As the pcode versions, the stand-alone edition of MicrobeMS is Matlab based, so the Matlab Compiler Runtime (MCR) is required. Please see How to install MicrobeMS and Downloading MicrobeMS for more details.
What is a database spectrum
A database (db) spectrum is a spectrum that has been created from individual mass spectra and ideally contains the spectral variances of biological and technical replicate spectra. Spectra used to compile a database spectrum are ideally collected from identical or at least taxonomically highly related microbial strains. Database spectra are created from pre-processed spectra, and their peak tables, using standardized parameters (see the description of database spectra for more details).