Frequently Asked Questions (FAQ) - Revision history

Laschp: /* What is the most actual version of MicrobeMS? */

2026-05-01T10:02:26Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 12:02, 1 May 2026
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	'''May. 2026''': MicrobeMS v.0.93 released		'''May. 2026''': MicrobeMS v.0.93 released

	* Minor edits: peak labels, error reporting, functionality ''more'' in cmpr, increased accuracy of peak detection, etc.		* Minor edits: peak labels, error reporting, functionality of button ''more'' in function ''cmpr'', increased accuracy of peak detection, etc.
	* Many code improvements & bug fixes		* Many code improvements & bug fixes

Laschp: /* What is the most actual version of MicrobeMS? */

2026-05-01T10:01:50Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 12:01, 1 May 2026
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	== What is the most actual version of MicrobeMS? ==		== What is the most actual version of MicrobeMS? ==

	The most actual version of the MicrobeMS software is MicrobeMS v. 0.92 from ~~January~~ 2026. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].		The most actual version of the MicrobeMS software is MicrobeMS v. 0.93 from May 2026. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].

	'''Jan. 2026''': MicrobeMS v.0.92 ~~released~~		'''May. 2026''': MicrobeMS v.0.93 released

			* Minor edits: peak labels, error reporting, functionality ''more'' in cmpr, increased accuracy of peak detection, etc.
			* Many code improvements & bug fixes

			'''Jan. 2026''': MicrobeMS v.0.92

	* [[Export XML Data\|''XML export filter'']] for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.		* [[Export XML Data\|''XML export filter'']] for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.
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	* Many code improvements & bug fixes		* Many code improvements & bug fixes

	'''Jun. 2025''': MicrobeMS v.0.90 ~~released~~		'''Jun. 2025''': MicrobeMS v.0.90

	* Major revisions of the function [[Unsupervised Hierarchical Cluster Analysis\|''Unsupervised hierarchical cluster analysis'']]		* Major revisions of the function [[Unsupervised Hierarchical Cluster Analysis\|''Unsupervised hierarchical cluster analysis'']]
	* Code improvements and bug fixes		* Code improvements and bug fixes

	'''Feb. 2025''': MicrobeMS v.0.89 ~~released~~		'''Feb. 2025''': MicrobeMS v.0.89

	* Spectral prep-processing functions revised, see [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing ''MicrobeMS - Spectral Pre-processing''] for details		* Spectral prep-processing functions revised, see [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing ''MicrobeMS - Spectral Pre-processing''] for details

Laschp: /* What is a database spectrum? */

2026-03-08T05:19:38Z

What is a database spectrum?

← Older revision		Revision as of 07:19, 8 March 2026
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	== What is a database spectrum? ==		== 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 [[Create database spectra\|database spectra ]] for more details).		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 [[Create database spectra\|database spectra]] for more details).

Laschp: /* I have installed MicrobeMS, but I would like to use also spectral databases */

2026-03-08T05:18:57Z

I have installed MicrobeMS, but I would like to use also spectral databases

← Older revision		Revision as of 07:18, 8 March 2026
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	== I have installed MicrobeMS, but I would like to use also spectral databases ==		== 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: [mailto:lasch@microbe-ms.com lasch@microbe-ms.com]<br>		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: [mailto:lasch@microbe-ms.com lasch@microbe-ms.com].<br>

	'''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 [http~~://doi.org/10.5281/zenodo.~~163517 ''A MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch Institute (RKI)'']~~.		'''UPDATE Jan 2026''': An ''in silico'' MALDI-ToF MS database is available (CC-BY-NC-SA license). This database has been derived from UniprotKB proteomics databases, i.e. ultimately from microbial genomes. This database is still highly experimental and should not be used for diagnostic purposes. More details will follow in the near future.

			'''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.

	'''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 http~~://doi.org/10.5281/zenodo.~~582602~~] ~~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, [https://doi.org/10.1101/870089 ''Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data]'', bioRxiv (Dec 10, '''2018'''), doi:10.1101/870089.<br>
			The respective ''in silico'' database can be downloaded from Zenodo (1.5 GB!): [https://doi.org/10.5281/zenodo.3573996 ''In silico Database for Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹)''] Zenodo, December 13, 2019.<br> (cf. also [[Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases\|Identification analysis by means of LC-MS¹ and ''in silico'' databases]]).

	'''UPDATE Nov 2018''': The third update of the RKI MALDI-ToF MS database is available (Creatives Commons license, CC-BY-NC-SA).		'''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 https://doi.org/10.5281/zenodo.1880975] for details.		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 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,~~ [~~https~~://doi.org/10.~~1101~~/~~870089 ''Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹) and in silico Peptide Mass Data]'', bioRxiv (Dec 10, '''2018'''), doi:10~~.~~1101/870089.<br>~~		'''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 http://doi.org/10.5281/zenodo.582602] for details.
	~~The respective ''in silico'' database can be downloaded from Zenodo (1.5 GB!): [https~~://doi.org/10.5281/zenodo.~~3573996 ''In silico Database~~ for ~~Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS¹)''] Zenodo, December 13, 2019.<br> (cf~~. ~~also [[Identification Analysis by Means of LC-MS¹ and ''in silico'' Databases\|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.~~		'''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 [http://doi.org/10.5281/zenodo.163517 ''A MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch Institute (RKI)''].

	~~'''UPDATE Jan 2026''': An ''in silico~~'' MALDI-ToF ~~MS database is available~~ (~~CC-BY-NC-SA license~~). This database has been derived from UniprotKB proteomics databases, i.e. ultimately from microbial genomes. This database is still highly experimental and should not be used for diagnostic purposes. More details will follow in the near future.

	== What is a database spectrum? ==		== 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 [[Create database spectra\|database spectra ]] for more details).		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 [[Create database spectra\|database spectra ]] for more details).

Laschp: /* What is the most actual version of MicrobeMS? */

2026-03-08T05:16:45Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 07:16, 8 March 2026
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	'''Jun. 2025''': MicrobeMS v.0.90 released		'''Jun. 2025''': MicrobeMS v.0.90 released

	* Major revisions of the function cluster analysis		* Major revisions of the function [[Unsupervised Hierarchical Cluster Analysis\|''Unsupervised hierarchical cluster analysis'']]
	* Code improvements and bug fixes		* Code improvements and bug fixes

Laschp: /* What is the most actual version of MicrobeMS? */

2026-03-08T05:15:23Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 07:15, 8 March 2026
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	'''Jan. 2026''': MicrobeMS v.0.92 released		'''Jan. 2026''': MicrobeMS v.0.92 released

	* [[Export XML Data\|XML export filter]] for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.		* [[Export XML Data\|''XML export filter'']] for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.
	* New functionalities of the software function [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]: introducing a MBT like identification method		* New functionalities of the software function [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|''Microbial identification based on mass spectral libraries and interspectral distances'']]: introducing a MBT like identification method
	* [[MALDI Quality Tests\|Quality test]] function significantly revised		* [[MALDI Quality Tests\|Quality test]] function significantly revised
	* Many code improvements & bug fixes		* Many code improvements & bug fixes

Laschp: /* What is the most actual version of MicrobeMS? */

2026-03-08T05:14:31Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 07:14, 8 March 2026
Line 9:		Line 9:
	'''Jan. 2026''': MicrobeMS v.0.92 released		'''Jan. 2026''': MicrobeMS v.0.92 released

	* XML export filter for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.		* [[Export XML Data\|XML export filter]] for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.
	* New functionalities of the software function Microbial identification based on mass spectral libraries and interspectral distances: introducing a MBT like identification method		* New functionalities of the software function [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]: introducing a MBT like identification method
	* Quality ~~tests~~ function significantly revised		* [[MALDI Quality Tests\|Quality test]] function significantly revised
	* Many code improvements & bug fixes		* Many code improvements & bug fixes

Laschp: /* What is the most actual version of MicrobeMS? */

2026-01-17T15:43:20Z

What is the most actual version of MicrobeMS?

Laschp: /* What is the most actual version of MicrobeMS? */

2026-01-17T15:41:57Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 17:41, 17 January 2026
Line 5:		Line 5:
	== What is the most actual version of MicrobeMS? ==		== What is the most actual version of MicrobeMS? ==

	The most actual version of the MicrobeMS software is MicrobeMS v. 0.90 from ~~June 2025~~. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].		The most actual version of the MicrobeMS software is MicrobeMS v. 0.92 from January 2026. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].

	'''Jan. 2026''': MicrobeMS v.0.92 released - bug fixes:		'''Jan. 2026''': MicrobeMS v.0.92 released - bug fixes:

Laschp: /* What is the most actual version of MicrobeMS? */

2026-01-17T15:41:12Z

What is the most actual version of MicrobeMS?

← Older revision		Revision as of 17:41, 17 January 2026
Line 9:		Line 9:
	'''Jan. 2026''': MicrobeMS v.0.92 released - bug fixes:		'''Jan. 2026''': MicrobeMS v.0.92 released - bug fixes:

	* ~~Major revisions~~ of the function ~~cluster analysis~~		* XML export filter for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.
	* ~~Code~~ improvements ~~and~~ bug fixes		* New functionalities of the software function Microbial identification based on mass spectral libraries and interspectral distances: introducing a MBT like identification method
			* Quality tests function significantly revised
			* Many code improvements & bug fixes

	'''Jun. 2025''': MicrobeMS v.0.90 released - bug fixes:		'''Jun. 2025''': MicrobeMS v.0.90 released - bug fixes:

← Older revision		Revision as of 17:43, 17 January 2026
Line 7:		Line 7:
	The most actual version of the MicrobeMS software is MicrobeMS v. 0.92 from January 2026. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].		The most actual version of the MicrobeMS software is MicrobeMS v. 0.92 from January 2026. The MicrobeMS software is continuously being developed further and can be downloaded [[download_MicrobeMS\|here]].

	'''Jan. 2026''': MicrobeMS v.0.92 released ~~- bug fixes:~~		'''Jan. 2026''': MicrobeMS v.0.92 released

	* XML export filter for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.		* XML export filter for exporting MALDI-ToF MS spectrum data in to a format suitable for utilization of the MicrobeNet solution of the CDC's.
Line 14:		Line 14:
	* Many code improvements & bug fixes		* Many code improvements & bug fixes

	'''Jun. 2025''': MicrobeMS v.0.90 released ~~- bug fixes:~~		'''Jun. 2025''': MicrobeMS v.0.90 released

	* Major revisions of the function cluster analysis		* Major revisions of the function cluster analysis
	* Code improvements and bug fixes		* Code improvements and bug fixes

	'''Feb. 2025''': MicrobeMS v.0.89 released ~~- New functions and bug fixes:~~		'''Feb. 2025''': MicrobeMS v.0.89 released

	* Spectral prep-processing functions revised, see [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing ''MicrobeMS - Spectral Pre-processing''] for details		* Spectral prep-processing functions revised, see [https://wiki-ms.microbe-ms.com/index.php?title=Spectral_Pre-processing ''MicrobeMS - Spectral Pre-processing''] for details
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	* Code improvements and bug fixes		* Code improvements and bug fixes

	'''Feb. 2017''': New functions and ~~bugfixes~~ of version 0.80 (selection):		'''Feb. 2017''': New functions and bug fixes of version 0.80 (selection):

	* Re-designed interface to the NeuroDeveloper, a software for spectral analysis by artificial neural networks		* Re-designed interface to the NeuroDeveloper, a software for spectral analysis by artificial neural networks