Frequently Asked Questions (FAQ)
- 1 What is MicrobeMS?
- 2 What is the most actual version of MicrobeMS?
- 3 Is there a stand-alone version of MicrobeMS available?
- 4 MicrobeMS for LINUX. Can MicrobeMS be used under LINUX?
- 5 What is the Matlab component runtime (MCR) and why I need to install this software?
- 6 Why I need to install the MCR 2014a 64-bit and not a more actual version?
- 7 I have installed MicrobeMS, but I would like to use also spectral databases
- 8 What is a database spectrum?
What is MicrobeMS?
The software package available from MicrobeMS is a program that has been initially designed 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 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
Please refer also to the MicrobeMS website for more information.
Is there a stand-alone version of MicrobeMS available?
Yes, since November 2016 a stand-alone version of the MicrobeMS toolbox is available. The MicrobeMS stand alone-runs under Windows 7/8/8.1 and 10. As previous pcode versions, the stand-alone edition of MicrobeMS is Matlab based, so the free Matlab Compiler Runtime environment (MCR 2014a 64-bit) will be 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 Nov. 2019. This software version has been tested under Debian version 10 (code name Buster) and is available as a Matlab pcode toolbox, which means that Matlab plus two Matlab toolboxes (Statistics and Bioinformatics) are required. Further information can be found here.
What is the Matlab component runtime (MCR) and why I need to install this software?
MicrobeMS is a 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 for free of charge from the Mathworks website. It is important that the version of the MCR that runs the application on the target computer must be compatible with the version of the Matlab compiler used (i.e. MCR 2014a Windows 64-bit must be installed in order to use the actual version of MicrobeMS [v. 0.82])
Why I need to install the MCR 2014a 64-bit and not a more actual version?
First of all, MicrobeMS has been compiled with the Matlab compiler of Matlab version R2014a (Windows 64-bit). But why not a more actual compiler version has been used?
The answer to this question consists of two parts:
Firstly, with new Matlab versions new functions are usually introduced while existing functions may be modified or even removed. These changes require therefore extensive checks for source code compatibility when migrating to a newer Matlab / Matlab compiler version. Secondly, with release R2014b The Mathworks introduced major changes of the underlying graphics libraries, see https://de.mathworks.com/help/matlab/graphics_transition/major-graphics-changes-in-r2014b.html for details. I have noted that these changes resulted in performance problems, see https://de.mathworks.com/matlabcentral/answers/203918-slow-plotting-performance-starting-from-matlab-r2014b as a example.
With this in mind, I decided to wait until the mentioned performance problems are solved by hardware evolution, i.e. to wait until faster hardware solved the problem by itself.
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: 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 second update of the RKI MALDI-TOF MS database is available (Creatives Commons license, CC-BY-NC-SA). The RKI database v.3 contains altogether 6264 mass spectra from 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 the diagnostics 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 its native 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)
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).