Create database spectra - Revision history

Laschp: /* Producing database spectra */

2025-06-06T14:43:59Z

Producing database spectra

← Older revision		Revision as of 16:43, 6 June 2025
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	3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|''class assignment'']]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' → ''class X'' from the ''Edit'' pulldown menu.		3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|''class assignment'']]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' → ''class X'' from the ''Edit'' pulldown menu.

	4. As a result database spectra are created from peak lists produced from series of pre-processed mass spectra. The parameters used for spectral pre-processing and peak detection are stored in the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''~~settings~~.opt'']]. When the procedure is finished a window entitled ''view/edit metadata and pre-processing parameters'' comes up which offers the possibility to inspect and modify the metadata information. Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and assigned.		4. As a result database spectra are created from peak lists produced from series of pre-processed mass spectra. The parameters used for spectral pre-processing and peak detection are stored in the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''microbems.opt'']]. When the procedure is finished a window entitled ''view/edit metadata and pre-processing parameters'' comes up which offers the possibility to inspect and modify the metadata information. Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and assigned.

	5. An option to create series of database spectra in an automated way is available from the option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pull down menu). A window entitled ''create db spectra'' offers the possibility to indicate indices of the mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in the second line. Press ''start'' when finished.		5. An option to create series of database spectra in an automated way is available from the option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pull down menu). A window entitled ''create db spectra'' offers the possibility to indicate indices of the mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in the second line. Press ''start'' when finished.

Laschp: /* Producing database spectra */

2025-03-27T09:33:02Z

Producing database spectra

← Older revision		Revision as of 11:33, 27 March 2025
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	4. As a result database spectra are created from peak lists produced from series of pre-processed mass spectra. The parameters used for spectral pre-processing and peak detection are stored in the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''settings.opt'']]. When the procedure is finished a window entitled ''view/edit metadata and pre-processing parameters'' comes up which offers the possibility to inspect and modify the metadata information. Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and assigned.		4. As a result database spectra are created from peak lists produced from series of pre-processed mass spectra. The parameters used for spectral pre-processing and peak detection are stored in the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''settings.opt'']]. When the procedure is finished a window entitled ''view/edit metadata and pre-processing parameters'' comes up which offers the possibility to inspect and modify the metadata information. Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and assigned.

	5. An option to create series of database spectra in an automated way is available from the option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' ~~pulldown~~ menu). A window entitled ''create db spectra'' offers the possibility to indicate indices of the mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in the second line. Press ''start'' when finished.		5. An option to create series of database spectra in an automated way is available from the option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pull down menu). A window entitled ''create db spectra'' offers the possibility to indicate indices of the mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in the second line. Press ''start'' when finished.

	== Related topics ==		== Related topics ==

Laschp: /* Producing database spectra */

2024-12-16T12:24:40Z

Producing database spectra

← Older revision		Revision as of 14:24, 16 December 2024
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	== Producing database spectra ==		== Producing database spectra ==

	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|''load spectra'']] (Bruker data file format),		1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|''load spectra'']] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|''import spectra from mzXML data'']], or the ''load MS multifile'' options of the ''File'' pulldown menu.
	[[Import Mass Spectra in a mzXML Data Format\|''import spectra from mzXML data'']], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	[[File:batch-dbspectra.jpg\|\|right\|Screenshot of the window ''create db spectra'']]		[[File:batch-dbspectra.jpg\|\|right\|Screenshot of the window ''create db spectra'']]
	2. To produce a database spectrum select the respective mass spectra in the listbox at the		2. To produce a database spectrum select the respective mass spectra in the listbox at the top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <Shift> key while selecting.
	top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra
	hold the <Shift> key while selecting.

	3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from		3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|''class assignment'']]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' → ''class X'' from the ''Edit'' pulldown menu.
	the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra,
	i.e. from spectra with a [[Class Assignment\|''class assignment'']]. Labeling, or class assignment, can be carried out
	by selecting the appropriate spectra and choosing ''class assignments'' → ''class X'' from
	the ''Edit'' pulldown menu.

	4. As a result database spectra are created from peak lists produced from series of pre-processed		4. As a result database spectra are created from peak lists produced from series of pre-processed mass spectra. The parameters used for spectral pre-processing and peak detection are stored in the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''settings.opt'']]. When the procedure is finished a window entitled ''view/edit metadata and pre-processing parameters'' comes up which offers the possibility to inspect and modify the metadata information. Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and assigned.
	mass spectra. The parameters used for spectral pre-processing and peak detection are stored in
	the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''settings.opt'']].
	When the procedure is finished a window entitled ''view/edit metadata and pre-processing''
	''parameters'' comes up which offers the possibility to inspect and modify the metadata information.
	Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and
	assigned.

	5. An option to create series of database spectra in an automated way is available from the		5. An option to create series of database spectra in an automated way is available from the option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pulldown menu). A window entitled ''create db spectra'' offers the possibility to indicate indices of the mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in the second line. Press ''start'' when finished.
	option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pulldown menu).
	A window entitled ''create db spectra'' offers the possibility to indicate indices of the
	mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a
	second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in
	the second line. Press ''start'' when finished.

	== Related topics ==		== Related topics ==

Laschp: /* Introduction */

2024-12-16T09:55:38Z

Introduction

← Older revision		Revision as of 11:55, 16 December 2024
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	== Introduction ==		== Introduction ==

	Database spectra are the preferred type of database entries in MicrobeMS. Such database spectra constitute the spectral references of a microbial library. Ideally database spectra are obtained from multiple measurements of the bacterial isolate under study in order to cover the spectral variability contained in the spectra of biological and technical replicates. The number of individual spectra used for database spectrum generation should ideally vary between 12 and 20 and should include data from biological ~~(3x)~~ and technical ~~(4x)~~ replicates.		Database spectra are the preferred type of database entries in MicrobeMS. Such database spectra constitute the spectral references of a microbial library. Ideally database spectra are obtained from multiple measurements of the bacterial isolate under study in order to cover the spectral variability contained in the spectra of biological and technical replicates. The number of individual spectra used for database spectrum generation should ideally vary between 12 and 20 and should include data from 3 biological and 4 technical replicates.

	The concept of database spectra involves automated generation of peak tables from spectral measurement series in which information about peak positions (m/z), normalized peak intensities and peak frequencies are obtained.		The concept of database spectra involves automated generation of peak tables from spectral measurement series in which information about peak positions (m/z), normalized peak intensities and peak frequencies are obtained.

Laschp: /* Introduction */

2024-12-16T09:54:23Z

Introduction

← Older revision		Revision as of 11:54, 16 December 2024
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	== Introduction ==		== Introduction ==

	Database spectra are the preferred type of database entries in MicrobeMS. Such database spectra constitute the spectral references of a microbial library. Ideally database spectra are obtained from multiple measurements of the bacterial isolate under study in order to cover the spectral variability contained in the spectra of biological and technical replicates.		Database spectra are the preferred type of database entries in MicrobeMS. Such database spectra constitute the spectral references of a microbial library. Ideally database spectra are obtained from multiple measurements of the bacterial isolate under study in order to cover the spectral variability contained in the spectra of biological and technical replicates. The number of individual spectra used for database spectrum generation should ideally vary between 12 and 20 and should include data from biological (3x) and technical (4x) replicates.

	The concept of database spectra involves automated generation of peak tables from spectral measurement series in which information about peak positions (m/z), normalized peak intensities and peak frequencies are obtained.		The concept of database spectra involves automated generation of peak tables from spectral measurement series in which information about peak positions (m/z), normalized peak intensities and peak frequencies are obtained.

Laschp: /* Introduction */

2024-12-16T09:51:06Z

Introduction

← Older revision		Revision as of 11:51, 16 December 2024
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	Mass peak tables from unknown microbial strains are then compared by pattern matching algorithms against a library of database spectra. The results of the pattern matching analyses can be provided as a matching rank rank list, either in a text, or a HTML format. These reports are easy to interpret and allow microbial identification down to the species level.		Mass peak tables from unknown microbial strains are then compared by pattern matching algorithms against a library of database spectra. The results of the pattern matching analyses can be provided as a matching rank rank list, either in a text, or a HTML format. These reports are easy to interpret and allow microbial identification down to the species level.

	The database spectrum in the strict sense is represented by a simple average spectrum with a special type of peak table. Peak tables of database spectra contain the relevant information for the identification algorithms. Unlike the peak tables obtained from single experimental mass spectra the peak tables of database spectra contain also peak frequency information.		The database spectrum in the strict sense is represented by a simple average spectrum with a special type of peak table. Peak tables of database spectra contain the relevant information for the identification algorithms. Unlike the peak tables obtained from single experimental mass spectra the peak tables of database spectra contain also the peak frequency information.

	== Producing database spectra ==		== Producing database spectra ==

Laschp: /* Producing database spectra */

2024-12-16T09:49:31Z

Producing database spectra

Laschp: /* Related topics */

2024-12-16T09:44:52Z

Laschp: /* Related topics */

2024-12-16T09:44:34Z

Laschp: /* Related topics */

2024-12-16T09:44:11Z

← Older revision		Revision as of 11:44, 16 December 2024
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	== Related topics ==		== Related topics ==

	* [[Description of MicrobeMS' main parameter file 'microbems.opt'\|Modify parameters for automated generation of data base spectra]] ''microbems.opt''		* [[Description of MicrobeMS' main parameter file 'microbems.opt'\|Modify parameters for automated generation of data base spectra]] (edit ''microbems.opt'')
	* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]		* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]
	* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]		* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]

← Older revision		Revision as of 11:44, 16 December 2024
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	== Related topics ==		== Related topics ==

	* [[Description of MicrobeMS' main parameter file 'microbems.opt'\|Modify parameters for automated generation of data base spectra ''microbems.opt'']]		* [[Description of MicrobeMS' main parameter file 'microbems.opt'\|Modify parameters for automated generation of data base spectra]] ''microbems.opt''
	* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]		* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]
	* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]		* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]

← Older revision		Revision as of 11:44, 16 December 2024
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	== Related topics ==		== Related topics ==

	* [[Modify parameters for automated generation of data base spectra]]		* [[Description of MicrobeMS' main parameter file 'microbems.opt'\|Modify parameters for automated generation of data base spectra ''microbems.opt'']]
	* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]		* [[Data_Format_of_Peak_List_Files#structure array dbs \| Format of a database spectrum]]
	* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]		* [[Data_Format_of_Peak_List_Files#peak table format \| Format of peak tables]]

← Older revision		Revision as of 11:49, 16 December 2024
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	== Producing database spectra ==		== Producing database spectra ==

	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format),		1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|''load spectra'']] (Bruker data file format),
	[[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.		[[Import Mass Spectra in a mzXML Data Format\|''import spectra from mzXML data'']], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	[[File:batch-dbspectra.jpg\|\|right\|Screenshot of the window ''create db spectra'']]		[[File:batch-dbspectra.jpg\|\|right\|Screenshot of the window ''create db spectra'']]
	2. To produce a database spectrum select the respective mass spectra in the listbox at the		2. To produce a database spectrum select the respective mass spectra in the listbox at the
	top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra		top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra
	hold the <~~shift~~> key while selecting.		hold the <Shift> key while selecting.

	3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from		3. Start the procedure by selecting ''create database spectra'' → ''from selection'' from
	the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra,		the ''Analysis'' pull down menu. Database spectra can be also created from labeled spectra,
	i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out		i.e. from spectra with a [[Class Assignment\|''class assignment'']]. Labeling, or class assignment, can be carried out
	by selecting the appropriate spectra and choosing ''class assignments'' &rarr ''class X'' from		by selecting the appropriate spectra and choosing ''class assignments'' → ''class X'' from
	the ''Edit'' pulldown menu.		the ''Edit'' pulldown menu.

	4. As a result database spectra are created from peak lists produced from series of pre-processed		4. As a result database spectra are created from peak lists produced from series of pre-processed
	mass spectra. The parameters used for spectral pre-processing and peak detection are stored in		mass spectra. The parameters used for spectral pre-processing and peak detection are stored in
	the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|settings.opt]].		the MicrobeMS configuration file [[Description of MicrobeMS' main parameter file 'microbems.opt'\|''settings.opt'']].
	When the procedure is finished a window entitled ''view/edit metadata and pre-processing''		When the procedure is finished a window entitled ''view/edit metadata and pre-processing''
	''parameters'' comes up which offers the possibility to inspect and modify the metadata information.		''parameters'' comes up which offers the possibility to inspect and modify the metadata information.
	Furthermore, a new file id in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and		Furthermore, a new file ID in the format dbspec-DD-MON-YEAR-HR-MI-SE.XXX will be created and
	assigned.		assigned.

	5. An option to create series of database spectra in an automated way is available from the		5. An option to create series of database spectra in an automated way is available from the
	option ''create database spectra'' &rarr ''db spec batch mode'' (''Analysis'' pulldown menu).		option ''create database spectra'' → ''db spec batch mode'' (''Analysis'' pulldown menu).
	A window entitled ''create db spectra'' offers the possibility to indicate indices of the		A window entitled ''create db spectra'' offers the possibility to indicate indices of the
	mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a		mass spectra to be used. For example, to create a database spectrum from spectra 1-8 and to create a
	second database spectrum from spectra 12-14 indicate 1 8 in the first line and 12 14 in		second database spectrum from spectra 12-14 indicate 1 8 in the first line, and 12 14 in
	the second line. Press ''start'' when finished.		the second line. Press ''start'' when finished.