Frequently Asked Questions (FAQ)
What is MicrobeMS?
The MicrobeMS software package is a program initially 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.
What is the most actual version of MicrobeMS?
The most actual version of the MicrobeMS software is MicrobeMS v. 0.82 from December 2019. The software can be downloaded here.
Feb. 2017: New functions and bugfixes of version 0.80 (selection):
- Re-designed interface to the NeuroDeveloper, a software for spectral analysis by 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
- Many code improvements & bug fixes.
Nov. 2019: New functions and bug fixes of version 0.82:
- Further optimization of the function Microbial identification based on mass spectral libraries and interspectral distances: Speed improvement by a factor of ~2 compared with version 0.80.
- MicrobeMS v. 0.82 allows analysis of LC-MS¹ spectra from microorganisms. Identification analysis of the LC-MS¹ data requires a synthetic in silico database of peptide mass data calculated from microbial genomes (see see Preprint Lasch P, Schneider A, Blumenscheit C and Doellinger J, Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data, bioRxiv (Dec 10, 2018), doi:10.1101/870089.)
- Code improvements and bug fixes
Feb. 2023: Coming soon - a new version of MicrobeMS will be released in the very near future
Is there a standalone version of MicrobeMS?
Yes, a standalone version of the MicrobeMS toolbox has been available since November 2016. The MicrobeMS standalone runs on Windows 7/8/8.1/10 and 1a. Like previous pcode versions, the stand-alone version of MicrobeMS is based on Matlab, so the free Matlab Compiler Runtime environment (MCR 2014a 64-bit) is required. Please see How to install MicrobeMS and Downloading MicrobeMS for more details.
MicrobeMS for LINUX. Can MicrobeMS be used under LINUX?
A LINUX version of MicrobeMS has been released in November 2009. This software version has been tested on Debian version 10 (codename Buster) and is available as a Matlab pcode toolbox, i.e. it requires Matlab plus two Matlab toolboxes (Statistics and Bioinformatics). More information can be found here.
What is the Matlab Component Runtime (MCR) and why do I need to install it?
MicrobeMS is Matlab based software. The Matlab component runtime is a standalone set of shared libraries that enables the execution of compiled Matlab applications or components on computers that do not have Matlab installed. The Matlab Component Runtime (MCR) is available at no charge from the Mathworks Web site. It is important that the version of MCR that runs the application on the target computer is compatible with the version of the Matlab compiler used (i.e. MCR 2014a Windows 64-bit must be installed to use the current version of MicrobeMS [v. 0.82]).
Why I do need to install the MCR 2014a 64-bit and not a more recent version?
First of all, MicrobeMS has been compiled with the Matlab compiler of Matlab version R2014a (Windows 64-bit). But why was a more recent compiler version not used?
The answer to this question has two parts:
First, new Matlab versions usually introduce new features, while existing features may be modified or even removed. These changes require extensive source code compatibility checks when migrating to a newer Matlab / Matlab compiler version. Second, with the R2014b release, The Mathworks introduced major changes to the underlying graphics libraries, see https://de.mathworks.com/help/matlab/graphics_transition/major-graphics-changes-in-r2014b.html for details. I noticed that these changes caused performance problems, see https://de.mathworks.com/matlabcentral/answers/203918-slow-plotting-performance-starting-from-matlab-r2014b for an example.
With this in mind, I decided to wait for the performance problems to be solved by hardware evolution, i.e. to wait for faster hardware to solve the problem by itself.
I have installed MicrobeMS, but I would like to use also spectral databases
Databases of microbial mass spectra are not provided with the software (except some test spectra of selected Escherichia coli strains). For a limited number of users we provide spectral databases from our Yersinia and Bacillus study on personal request (signing of a data transfer agreement - DTA - is required). Please send an email with your request to the following address: firstname.lastname@example.org
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.
UPDATE Nov 2018: The third update of the RKI MALDI-TOF MS database is available (Creatives Commons license, CC-BY-NC-SA). The RKI database v.3 contains a total of 6264 mass spectra of highly pathogenic (i.e. biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Yersinia pestis, Burkholderia mallei, Burkholderia pseudomallei and Francisella tularensis as well as a selection of spectra from their close and more distant relatives. The database can be used as a reference for diagnosis of BSL-3 bacteria using proprietary and free software packages for MALDI-TOF MS-based microbial identification. Spectral data are distributed as a 7-zip archive that contains the original mass spectra in the original data format (Bruker Daltonics), see https://doi.org/10.5281/zenodo.1880975 for details.
UPDATE Dec 2019: The concept of microbial identification by means of MALDI-TOF mass spectrometry measurements of cultivated microbial cells and comparison with entries of a spectral library has been adapted for LC-MS¹ based microbial identification, see Preprint Lasch P, Schneider A, Blumenscheit C and Doellinger J, Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data, bioRxiv (Dec 10, 2018), doi:10.1101/870089.
The respective in silico database can be downloaded from Zenodo (1.5 GB!): In silico Database for Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) Zenodo, December 13, 2019.
(cf. also Identification analysis by means of LC-MS¹ and in silico databases)
UPDATE May 2023: MALDI-TOF MS database version 4 is available, again under the Creatives Commons license (CC-BY-NC-SA). The RKI Database v.4 now contains a total of 11055 MALDI-ToF mass spectra from 1599 microbial strains of highly pathogenic (i.e. biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Brucella melitensis, Yersinia pestis, Burkholderia mallei / pseudomallei and Francisella tularensis as well as a selection of spectra of their close and distant relatives, for details see https://doi.org/10.5281/zenodo.7702375.
What is a database spectrum?
A database (db) spectrum is a spectrum created from individual mass spectra, ideally containing the spectral variances of biological and technical replicate spectra. Spectra used to construct a database spectrum are ideally collected from identical or at least taxonomically closely 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).