Description of MicrobeMS' main parameter file 'microbems.opt' - Revision history

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

Laschp: /* Contents of microbems.opt */

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Contents of microbems.opt

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	== Contents of ''microbems.opt'' ==		== Contents of ''microbems.opt'' ==

	The file ''microbems.opt'' is s simple text file which can be edited by text editors like Notepad, ~~Textpad, or~~ Notepad++. The following table shows an example of the contents of ''microbems.opt'':		The file ''microbems.opt'' is s simple text file which can be edited by text editors like Notepad, Notepad++, Nano, etc. The following table shows an example of the contents of ''microbems.opt'':

	<ul><ul>		<ul><ul>

Laschp: /* Introduction */

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Introduction

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	== Introduction ==		== Introduction ==

	This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.92. ~~Parameters~~ specified in this file may be different in earlier program versions.		This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.92. Note that parameters specified in this file may be different in earlier program versions.

	The file ''microbems.opt'' is a simple text file which is read upon initialization of MicrobeMS. It contains a number of program-wide parameters, quality test parameters and parameters required for auto-preprocessing and auto-peak detection from raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried when generating [[Create database spectra\|database spectra]] and in the [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|workflow for microbial identification based on mass spectral libraries and interspectral distances]].<br>		The file ''microbems.opt'' is a simple text file which is read upon initialization of MicrobeMS. It contains a number of program-wide parameters, quality test parameters and parameters required for auto-preprocessing and auto-peak detection from raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried when generating [[Create database spectra\|database spectra]] and in the [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|workflow for microbial identification based on mass spectral libraries and interspectral distances]].<br>

Laschp at 05:54, 8 March 2026

2026-03-08T05:54:33Z

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	== Introduction ==		== Introduction ==

	This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.92.		This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.92. Parameters specified in this file may be different in earlier program versions.

	The file ''microbems.opt'' is a simple text file which is read upon initialization of MicrobeMS. It contains a number of program-wide parameters, quality test parameters and parameters required for auto-preprocessing and auto-peak detection from raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried when generating [[Create database spectra\|database spectra]] and in the [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|workflow for microbial identification based on mass spectral libraries and interspectral distances]].<br>		The file ''microbems.opt'' is a simple text file which is read upon initialization of MicrobeMS. It contains a number of program-wide parameters, quality test parameters and parameters required for auto-preprocessing and auto-peak detection from raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried when generating [[Create database spectra\|database spectra]] and in the [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|workflow for microbial identification based on mass spectral libraries and interspectral distances]].<br>

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

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	* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''		* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''
	* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''		* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''
	* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks gives the maximum number of peaks in the database spectra (whereas ''npeaks'' is the last value of data.mkdb.ppr)		* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks gives the maximum number of peaks contained in the database spectra (whereas ''npeaks'' is the last value of data.mkdb.ppr)

	'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''		'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

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	* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''		* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''
	* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''		* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''
	* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks (the last value of data.mkdb.ppr) ~~gives the maximum number of peaks of database spectra~~		* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks gives the maximum number of peaks in the database spectra (whereas ''npeaks'' is the last value of data.mkdb.ppr)

	'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''		'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

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	'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''		'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''
	* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation		* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation
	* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), , see spectral pre-processing, [[Spectral Pre-processing#Smoothing\|smoothing]]		* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral Pre-processing#Smoothing\|smoothing]]
	* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, , for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]		* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]
	* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

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	* ''data.maldi.ppr'' - parameters used for peak picking of MALDI-ToF mass spectra, see [[Peak Detection\|peak detection]] for details		* ''data.maldi.ppr'' - parameters used for peak picking of MALDI-ToF mass spectra, see [[Peak Detection\|peak detection]] for details
	* ''data.lcms1.ppr'' - not used		* ''data.lcms1.ppr'' - not used

	'''Parameters used for auto-preprocessing and auto-peak detection when creating database spectra'''		'''Parameters used for auto-preprocessing and auto-peak detection when creating database spectra'''
	* ''data.mkdb.seq'' - defines the sequence of pre-processing steps when compiling database spectra, see [[Spectral Pre-processing#\|spectral pre-processing]]		* ''data.mkdb.seq'' - defines the sequence of pre-processing steps when compiling database spectra, see [[Spectral Pre-processing#\|spectral pre-processing]]
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	* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''		* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 ≤ data.mkdb.threshold ≤ 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''
	* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks (the last value of data.mkdb.ppr) gives the maximum number of peaks of database spectra		* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 ≤ data.mkdb.fmaxnpks ≤ 1'']; data.mkdb.fmaxnpks × npeaks (the last value of data.mkdb.ppr) gives the maximum number of peaks of database spectra

	'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''		'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''
	* ''data.ident.seq'' - defines the sequence of pre-processing steps, see [[Spectral Pre-processing#\|spectral pre-processing]]		* ''data.ident.seq'' - defines the sequence of pre-processing steps, see [[Spectral Pre-processing#\|spectral pre-processing]]
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	* ''data.ident.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]		* ''data.ident.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]
	* ''data.ident.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.ident.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.ident.cut'' - ~~useful to narrow~~ the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.ident.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]
	* ''data.ident.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Reduce_resolution\|reduce resolution]]		* ''data.ident.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Reduce_resolution\|reduce resolution]]
	* ''data.ident.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral Pre-processing#Auto-calibration\|auto-calibration]]		* ''data.ident.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral Pre-processing#Auto-calibration\|auto-calibration]]
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	* ''data.ident.pkf'' - name of the peak list file which will be automatically loaded by the function ''identification'', see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]		* ''data.ident.pkf'' - name of the peak list file which will be automatically loaded by the function ''identification'', see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]
	* ''data.ident.pth'' - path to the peak list file indicated, see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]] for details		* ''data.ident.pth'' - path to the peak list file indicated, see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]] for details

			'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''
			* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation
			* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), , see spectral pre-processing, [[Spectral Pre-processing#Smoothing\|smoothing]]
			* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, , for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]
			* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
			* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]
			* ''data.bdal.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Reduce_resolution\|reduce resolution]]
			* ''data.bdal.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral Pre-processing#Auto-calibration\|auto-calibration]]
			* ''data.bdal.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details
			* ''data.bdal.scores'' - log scores thresholds, required for visualization of identification results of ''score ranking lists'' according to the traffic light scheme
			* ''data.bdal.soi'' - scores thresholds, used for visualization of identification results of ''rank list analyses'' according to the traffic light scheme
			* ''data.bdal.ppm'' - defines the width of mass spectrum bins in ppm units

	'''Quality test (QT) parameters'''		'''Quality test (QT) parameters'''
	* ''data.qual.qtresvalthresh'' - QT scores thresholds, used for visualization of quality test results according to a traffic light scheme, defaults: 30 and 45		* ''data.qual.qtresvalthresh'' - QT scores thresholds, used for visualization of quality test results according to a traffic light scheme, defaults: 30 and 45

Laschp: /* Parameters stored in microbems.opt */

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Parameters stored in microbems.opt

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	* ''data.qual.nbins'' - number of bins for quality parameters, default value: 15		* ''data.qual.nbins'' - number of bins for quality parameters, default value: 15
	* ''data.qual.noiselvl'' - noise level settings, in the default settings the noise parameter may vary between 0.40 (almost perfect, score of 100) and 3.5 (failed, score of 0)		* ''data.qual.noiselvl'' - noise level settings, in the default settings the noise parameter may vary between 0.40 (almost perfect, score of 100) and 3.5 (failed, score of 0)
	* ''data.qual.noisewf'' - weighting factor of the QT parameter 'noise level' (default 0.30)		* ''data.qual.noisewf'' - weighting factor of the QT parameter ''noise level'' (default 0.30)
	* ''data.qual.baslnrrorlvl'' - baseline error settings, as per default settings the baseline parameter may vary between 1 (almost perfect, score of 100) and 45 (failed, score of 0)		* ''data.qual.baslnrrorlvl'' - baseline error settings, as per default settings the baseline parameter may vary between 1 (almost perfect, score of 100) and 45 (failed, score of 0)
	* ''data.qual.baslerrwf'' - weighting factor of the QT parameter 'baseline' level (default 0.15)		* ''data.qual.baslerrwf'' - weighting factor of the QT parameter ''baseline'' level (default 0.15)
	* ''data.qual.npeakslvl'' - number of peaks, in the default settings this parameter may vary between 8 (very poor, score of 0) and 50 (excellent, score of 100)		* ''data.qual.npeakslvl'' - number of peaks, in the default settings this parameter may vary between 8 (very poor, score of 0) and 50 (excellent, score of 100)
	* ''data.qual.npeakswf'' - weighting factor of the QT parameter 'number of peaks' (default 0.40)		* ''data.qual.npeakswf'' - weighting factor of the QT parameter ''number of peaks'' (default 0.40)
	* ''data.qual.respowerlvl'' - resolving power settings, the parameter may vary between 250 (very poor, score of 0) and 1100 (excellent, score of 100)		* ''data.qual.respowerlvl'' - resolving power settings, the parameter may vary between 250 (very poor, score of 0) and 1100 (excellent, score of 100)
	* ''data.qual.respowerwf'' - weighting factor of the QT parameter 'resolving power' (default 0.15)		* ''data.qual.respowerwf'' - weighting factor of the QT parameter ''resolving power'' (default 0.15)

	== Downloading ''microbems.opt'' ==		== Downloading ''microbems.opt'' ==

	The text file ''microbems.opt'' can be downloaded here (MicrobeMS v. 0.92 and later): https://wiki.microbe-ms.com/uploads/microbems.opt		The text file ''microbems.opt'' can be downloaded here (MicrobeMS v. 0.92 and later): https://wiki.microbe-ms.com/uploads/microbems.opt

Laschp: /* Parameters stored in microbems.opt */

2026-03-08T05:34:55Z

Parameters stored in microbems.opt

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	* ''data.qual.qtresvalthresh'' - QT scores thresholds, used for visualization of quality test results according to a traffic light scheme, defaults: 30 and 45		* ''data.qual.qtresvalthresh'' - QT scores thresholds, used for visualization of quality test results according to a traffic light scheme, defaults: 30 and 45
	* ''data.qual.nbins'' - number of bins for quality parameters, default value: 15		* ''data.qual.nbins'' - number of bins for quality parameters, default value: 15
	* ''data.qual.noiselvl'' - noise level settings, in the default settings the noise parameter may vary between 0.20 (almost perfect, score of 100) and 6.0 (failed, score of 0)		* ''data.qual.noiselvl'' - noise level settings, in the default settings the noise parameter may vary between 0.40 (almost perfect, score of 100) and 3.5 (failed, score of 0)
	* ''data.qual.noisewf'' - weighting factor of the QT parameter 'noise level' (default 0.30)		* ''data.qual.noisewf'' - weighting factor of the QT parameter 'noise level' (default 0.30)
	* ''data.qual.baslnrrorlvl'' - baseline error settings, as per default settings the baseline parameter may vary between ~~0.15~~ (almost perfect, score of 100) and 40 (failed, score of 0)		* ''data.qual.baslnrrorlvl'' - baseline error settings, as per default settings the baseline parameter may vary between 1 (almost perfect, score of 100) and 45 (failed, score of 0)
	* ''data.qual.baslerrwf'' - weighting factor of the QT parameter 'baseline' level (default 0.15)		* ''data.qual.baslerrwf'' - weighting factor of the QT parameter 'baseline' level (default 0.15)
	* ''data.qual.npeakslvl'' - number of peaks, in the default settings this parameter may vary between 14 (very poor, score of 0) and 70 (excellent, score of 100)		* ''data.qual.npeakslvl'' - number of peaks, in the default settings this parameter may vary between 8 (very poor, score of 0) and 50 (excellent, score of 100)
	* ''data.qual.npeakswf'' - weighting factor of the QT parameter 'number of peaks' (default 0.40)		* ''data.qual.npeakswf'' - weighting factor of the QT parameter 'number of peaks' (default 0.40)
	* ''data.qual.respowerlvl'' - resolving power settings, the parameter may vary between ~~200~~ (very poor, score of 0) and ~~1200~~ (excellent, score of 100)		* ''data.qual.respowerlvl'' - resolving power settings, the parameter may vary between 250 (very poor, score of 0) and 1100 (excellent, score of 100)
	* ''data.qual.respowerwf'' - weighting factor of the QT parameter 'resolving power' (default 0.15)		* ''data.qual.respowerwf'' - weighting factor of the QT parameter 'resolving power' (default 0.15)

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	'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''		'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''
	* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation		* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation
	* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), , see spectral pre-processing, [[Spectral Pre-processing#Smoothing\|smoothing]]		* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral Pre-processing#Smoothing\|smoothing]]
	* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, , for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]		* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral Pre-processing#Baseline correction\|baseline correction]]
	* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]

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	'''Parameters used for auto-preprocessing and auto-peak detection when creating database spectra'''		'''Parameters used for auto-preprocessing and auto-peak detection when creating database spectra'''
	* ''data.mkdb.seq'' - defines the sequence of pre-processing steps when compiling database spectra, see [[Spectral Pre-processing#\|spectral pre-processing]]		* ''data.mkdb.seq'' - defines the sequence of pre-processing steps when compiling database spectra, see [[Spectral Pre-processing#\|spectral pre-processing]]
	* ''data.mkdb.nsp'' - the number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[~~Spectral Pre~~-processing#Smoothing\|smoothing]]		* ''data.mkdb.nsp'' - the number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral_Pre-processing#Smoothing\|smoothing]]
	* ''data.mkdb.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Baseline correction~~\|baseline correction]]		* ''data.mkdb.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral_Pre-processing#Baseline_correction\|baseline correction]]
	* ''data.mkdb.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.mkdb.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.mkdb.cut'' - useful to narrow the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.mkdb.cut'' - useful to narrow the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]
	* ''data.mkdb.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Reduce_resolution~~\|reduce resolution]]		* ''data.mkdb.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral_Pre-processing#Reduce_resolution_(binning)\|reduce resolution]]
	* ''data.mkdb.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Auto-calibration~~\|auto-calibration]]		* ''data.mkdb.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral_Pre-processing#Autocalibration\|auto-calibration]]
	* ''data.mkdb.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details		* ''data.mkdb.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details
	* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''		* ''data.mkdb.int'' - if set to '''1''': create db spectra with intensities (non-barcode spectra), otherwise '''0'''
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	'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''		'''Parameters used for auto-preprocessing and auto-peak detection in the microbial identification workflow'''
	* ''data.ident.seq'' - defines the sequence of pre-processing steps, see [[Spectral Pre-processing#\|spectral pre-processing]]		* ''data.ident.seq'' - defines the sequence of pre-processing steps, see [[Spectral Pre-processing#\|spectral pre-processing]]
	* ''data.ident.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[~~Spectral Pre~~-processing#Smoothing\|smoothing]]		* ''data.ident.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral_Pre-processing#Smoothing\|smoothing]]
	* ''data.ident.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Baseline correction~~\|baseline correction]]		* ''data.ident.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral_Pre-processing#Baseline_correction\|baseline correction]]
	* ''data.ident.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.ident.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.ident.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.ident.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]
	* ''data.ident.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Reduce_resolution~~\|reduce resolution]]		* ''data.ident.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral_Pre-processing#Reduce_resolution_(binning)\|reduce resolution]]
	* ''data.ident.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Auto-calibration~~\|auto-calibration]]		* ''data.ident.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral_Pre-processing#Autocalibration\|auto-calibration]]
	* ''data.ident.hit'' - maximum number of hits displayed in score ranking lists, see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]		* ''data.ident.hit'' - maximum number of hits displayed in score ranking lists, see [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances\|Microbial identification based on mass spectral libraries and interspectral distances]]
	* ''data.ident.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details		* ''data.ident.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details
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	'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''		'''Parameters used for by the function [[Export XML Data\|Export XML Data]] and MBT like identification'''
	* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation		* ''data.bdal.seq'' - defines the sequence of pre-processing steps when creating peak tables for XML file generation
	* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[~~Spectral Pre~~-processing#Smoothing\|smoothing]]		* ''data.bdal.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral_Pre-processing#Smoothing\|smoothing]]
	* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Baseline correction~~\|baseline correction]]		* ''data.bdal.bas'' - defines parameters used for spectral baseline correction, for details see spectral pre-processing, [[Spectral_Pre-processing#Baseline_correction\|baseline correction]]
	* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]		* ''data.bdal.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization\|normalization]]
	* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]		* ''data.bdal.cut'' - narrows the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut\|cut]]
	* ''data.bdal.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Reduce_resolution~~\|reduce resolution]]		* ''data.bdal.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral_Pre-processing#Reduce_resolution_(binning)\|reduce resolution]]
	* ''data.bdal.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[~~Spectral Pre~~-processing#~~Auto-calibration~~\|auto-calibration]]		* ''data.bdal.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral_Pre-processing#Autocalibration\|auto-calibration]]
	* ''data.bdal.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details		* ''data.bdal.ppr'' - peak detection parameters, see [[Peak Detection\|peak detection]] for details
	* ''data.bdal.scores'' - log scores thresholds, required for visualization of identification results of ''score ranking lists'' according to the traffic light scheme		* ''data.bdal.scores'' - log scores thresholds, required for visualization of identification results of ''score ranking lists'' according to the traffic light scheme