Mass Spectrometry Databases and Download MicrobeMS: Difference between pages

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MicrobeMS is available in two different editions: in (i) a stand-alone Windows 64-bit version requiring the Matlab Compiler Runtime (MCR) 64-bit and (ii) a Matlab pcode toolbox version requiring Matlab R2014 (Windows / Linux) or later.


== Introduction ==
Please note that you accept with downloading the [http://wiki.microbe-ms.com/uploads/license.txt: license conditions] of MicrobeMS.


Library based MS approaches for microbial identification require labeled sets of microbial mass spectra. Starting with version 0.82, MicrobeMS can work with experimental MALDI-TOF or LC-MS&sup1; mass spectra and their corresponding MS databases.<br>
=== MicrobeMS stand-alone (Windows) ===
The RKI databases of microbial MALDI-TOF mass spectra contain mass spectra of highly pathogenic (biosafety level 3, BSL-3) bacteria such as ''Bacillus anthracis'', ''Yersinia pestis'', ''Burkholderia mallei'', ''Burkholderia pseudomallei'', ''Brucella melitensis'' and ''Francisella tularensis'' as well as a selection of MALDI-TOF mass spectra of their close and distant relatives. The RKI mass spectral databases can be used as a reference for the diagnosis of BSL-3 bacteria using proprietary and free software packages for MALDI-TOF MS-based microbial identification. The databases are distributed as zip archives and contain the original mass spectra in their native data format (Bruker Daltonics). The MALDI-TOF MS databases are updated on a regular basis.<br>
The LC-MS&sup1; database is an ''in silico'' database compiled from Uni-Prot Knowledgebase resources (Uni-Prot/KB Swissprot and TrEMBL), for details see below).


== MALDI-TOF MS databases ==
<font color="red">'''NEW'''</font>  - Microbe MS 0.84 stand-alone 64-bit version (Windows, February 2022). To download the installer for this edition of MicrobeMS please use the link below:


The different versions of RKI biosafety level 3 (BSL-3) MALDI-TOF MS database can be downloaded from the following locations:
    [http://www.microbe-ms.com/microbe-ms/microbems.v.084.setup.zip: '''microbems.v.084.setup.zip''']


  1. [https://doi.org/10.5281/zenodo.7702375 Zenodo database version 4] (20230306):
Microbe MS 0.82 stand-alone 64-bit version (Windows) from January 2020:  
    Lasch P, St&auml;mmler M & Schneider A, (2023). Version 4 (20230306) of the
    MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
    Pathogenic Microorganisms from the Robert Koch-Institute (RKI).
    Zenodo. [https://doi.org/10.5281/zenodo.7702375 https://doi.org/10.5281/zenodo.7702375]
    Version Mar 06, 2023, creative commons CC BY-NC-SA 4.0 license


  2. [https://doi.org/10.5281/zenodo.1880975 Zenodo database version 3] (20181130):
    [http://www.microbe-ms.com/microbe-ms/microbems.v.082.setup.zip: '''microbems.v.082.setup.zip''']
    Lasch P, St&auml;mmler M & Schneider A, (2018). Version 3 (20181130) of the
    MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
    Pathogenic Microorganisms from the Robert Koch-Institute (RKI).  
    Zenodo. [https://doi.org/10.5281/zenodo.1880975 https://doi.org/10.5281/zenodo.1880975]
    Version Nov 30, 2018, creative commons CC BY-NC-SA 4.0 license


  3. [https://www.microbe-ms.com/microbe-ms/refdata/3745_Zenodo_v1.pdf Zenodo database version 2] (20170523):
Microbe MS 0.80 stand-alone 64-bit version (Windows) from February 2017:  
    Lasch P, St&auml;mmler M & Schneider , (2017). Version 2 (20170523) of the
    MALDI-TOF Mass Spectrometry Database for Identification and Classification of Highly
    Pathogenic Microorganisms from the Robert Koch-Institute (RKI).
    Zenodo. [http://doi.org/10.5281/zenodo.582602 http://doi.org/10.5281/zenodo.582602]
    Version May 23, 2017, creative commons CC BY-NC-SA 4.0 license


  4. [https://www.microbe-ms.com/microbe-ms/refdata/3280_Zenodo_v1.pdf Zenodo database version 1] (20161027):
    [http://www.microbe-ms.com/microbe-ms/microbems.v.080.setup.zip: '''microbems.v.080.setup.zip''']
    Lasch P, St&auml;mmler M & Schneider A, (2016). A MALDI-TOF Mass Spectrometry
    Database for Identification and Classification of Highly Pathogenic Microorganisms from
    the Robert Koch-Institute (RKI). Zenodo. [http://doi.org/10.5281/zenodo.163517 http://doi.org/10.5281/zenodo.163517]
    Version October 27, 2016, creative commons CC BY-NC-SA 4.0 license


== LC-MS&sup1; databases ==
Microbe MS 0.78 stand-alone 64-bit version (Windows) from November 2016:


The original concept of microbial identification by means of MALDI-TOF MS of cultivated microbial cells and spectral distance-based comparison with entries of a microorganism spectra library has been adapted for LC-MS&sup1; microbial identification, see this '''preprint''': Lasch P, Schneider A, Blumenscheit C and Doellinger J, [https://doi.org/10.1101/870089 ''Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS&sup1;) and in silico Peptide Mass Data]'', bioRxiv (Dec 10, '''2018'''), doi:10.1101/870089.<br>
    [http://www.microbe-ms.com/microbe-ms/microbemsv.078.setup.zip: '''microbems.v.078.setup.zip''']


  1. Lasch P, Schneider A, Blumenscheit C, Doellinger J. (2019). In silico Database for
=== MicrobeMS pcode (Windows and Linux) ===
    Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS&sup1;).
    Zenodo. [https://doi.org/10.5281/zenodo.3573996 https://doi.org/10.5281/zenodo.3573996]
    Version December 13, 2019, creative commons CC BY-NC-SA 4.0 license


Details can be found here: [[Identification Analysis by Means of LC-MS&sup1; and ''in silico'' Databases|Identification analysis by means of LC-MS&sup1; and ''in silico'' databases]]
MicrobeMS version 0.82 Matlab pcode for Windows and Linux (December 2019):
 
    [http://www.microbe-ms.com/microbe-ms/pcode-microbems-v082.zip: '''pcode-microbems-v082.zip''']
 
MicrobeMS version 0.78 Matlab pcode (Windows only!, November 2016):
 
    [http://www.microbe-ms.com/microbe-ms/pcode-microbems-v078.zip: '''pcode-microbems-v078.zip''']
 
=== Test Spectra and Databases ===
 
MALDI-TOF mass spectra from strains of ''Escherichia coli'' (zip archive, Bruker Daltonics MS data format):
 
    [http://www.microbe-ms.com/microbe-ms/refdata/Escherichia.zip '''Escherichia.zip''']
 
MALDI-TOF mass spectra from strains of ''Escherichia coli'' (Matlab data format, structure array ''spec''), <br>
see also [[Data_Format_of_Spectral_Multifiles|Data Format of Spectral Multifiles (*.muf)]]:
 
    [http://www.microbe-ms.com/microbe-ms/refdata/ecoli-filelist-oct16.muf: '''ecoli-filelist-oct16.muf''']
 
Peak list files obtained from mass spectra of strains of ''Escherichia coli'' (Matlab data format, structure array ''C''),<br>
see also [[Data_Format_of_Peak_List_Files|Peaks List Files (*.pkf)]] to obtain information on the file format
    [http://www.microbe-ms.com/microbe-ms/refdata/ecoli-peaklist-oct16.pkf: '''ecoli-peaklist-oct16.pkf''']
 
MS Excel template required to define and transfer metadata items into MicrobeMS,<br>
for file format information see [[Adding / Editing Metadata of MALDI-TOF Mass Spectral Data]]:
 
    [http://www.microbe-ms.com/microbe-ms/MALDI-Fields.xls: '''MALDI-Fields.xls''']
 
Download the most actual database versions with microbial MALDI-TOF MS, or synthetic LC-MS libraries:
 
    [[MALDI-TOF_Mass_Spectrometry_Database |MALDI-TOF Mass Spectrometry Databases from the RKI at ZENODO]]

Revision as of 15:39, 21 March 2023

MicrobeMS is available in two different editions: in (i) a stand-alone Windows 64-bit version requiring the Matlab Compiler Runtime (MCR) 64-bit and (ii) a Matlab pcode toolbox version requiring Matlab R2014 (Windows / Linux) or later.

Please note that you accept with downloading the license conditions of MicrobeMS.

MicrobeMS stand-alone (Windows)

NEW - Microbe MS 0.84 stand-alone 64-bit version (Windows, February 2022). To download the installer for this edition of MicrobeMS please use the link below: 

    microbems.v.084.setup.zip

Microbe MS 0.82 stand-alone 64-bit version (Windows) from January 2020: 

    microbems.v.082.setup.zip

Microbe MS 0.80 stand-alone 64-bit version (Windows) from February 2017: 

    microbems.v.080.setup.zip

Microbe MS 0.78 stand-alone 64-bit version (Windows) from November 2016: 

    microbems.v.078.setup.zip

MicrobeMS pcode (Windows and Linux)

MicrobeMS version 0.82 Matlab pcode for Windows and Linux (December 2019): 

    pcode-microbems-v082.zip

MicrobeMS version 0.78 Matlab pcode (Windows only!, November 2016): 

    pcode-microbems-v078.zip

Test Spectra and Databases

MALDI-TOF mass spectra from strains of Escherichia coli (zip archive, Bruker Daltonics MS data format): 

    Escherichia.zip

MALDI-TOF mass spectra from strains of Escherichia coli (Matlab data format, structure array spec),
see also Data Format of Spectral Multifiles (*.muf): 

    ecoli-filelist-oct16.muf

Peak list files obtained from mass spectra of strains of Escherichia coli (Matlab data format, structure array C),
see also Peaks List Files (*.pkf) to obtain information on the file format 

    ecoli-peaklist-oct16.pkf

MS Excel template required to define and transfer metadata items into MicrobeMS,
for file format information see Adding / Editing Metadata of MALDI-TOF Mass Spectral Data: 

    MALDI-Fields.xls

Download the most actual database versions with microbial MALDI-TOF MS, or synthetic LC-MS libraries: 

    MALDI-TOF Mass Spectrometry Databases from the RKI at ZENODO
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