Description of MicrobeMS' main parameter file 'microbems.opt': Difference between revisions

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== Introduction ==
== Introduction ==


'''Important notice''': This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.87 and later.
This section describes the format of the parameter file ''microbems.opt'' of MicrobeMS v. 0.87 and later.


The file ''microbems.opt'' is a simple text file which is read upon initialization of MicrobeMS. The file ''microbems.opt'' 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>   
The file ''microbems.opt'' can be usually found in one of the following directories:  
The parameter file can be usually found in one of the following directories:  


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


* Compiled Windows versions of MicrobeMS (MCR required): The file ''microbems.opt'' can usually be found in the directory C:\Users\Public\Documents\Matlab.
* Compiled Windows versions of MicrobeMS (MCR required): C:\Users\Public\Documents\Matlab.


* MicrobeMS installed as a Matlab toolbox (''pcode)'' on Windows operating systems (W7/W8/W8.1/W10/W11): root directory of the MicrobeMS toolbox, usually 'C:\Users\WindowsUserName\Documents\Matlab\mass' with WindowsUserName being the user's Windows name.
* MicrobeMS installed as a Matlab toolbox (''pcode)'' on Windows operating systems (Windows 7/8/8.1/10/11): root directory of the MicrobeMS toolbox, usually 'C:\Users\WindowsUserName\Documents\Matlab\mass' with WindowsUserName being the user's Windows name.


* LINUX versions (''pcode''): ''microbems.opt'' must reside in the pcode toolbox directory of MicrobeMS. Type >> which mass at the Matlab prompt when searching for this directory.
* LINUX versions (''pcode''): ''microbems.opt'' must reside in the pcode toolbox directory of MicrobeMS. Type<br>
  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; >> which mass <br>
  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; at the Matlab prompt when searching for this directory.


</ul></ul>
</ul></ul>


== Content 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, Textpad or Notepad++. The following table shows an example of the contents of ''microbems.opt'':


<ul><ul>
<ul><ul>
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  1                                                    ## data.mkdb.red
  1                                                    ## data.mkdb.red
                                                       ## data.mkdb.clb
                                                       ## data.mkdb.clb
  2000 13000 300 12000 7000 0.075 7.5 800 1 40         ## data.mkdb.ppr
  2000 13000 300 12000 7000 1 7.5 800 1 40             ## data.mkdb.ppr
  1                                                    ## data.mkdb.int
  1                                                    ## data.mkdb.int
  0.25                                                ## data.mkdb.threshold
  0.25                                                ## data.mkdb.threshold
Line 54: Line 56:
                                                       ## data.ident.clb
                                                       ## data.ident.clb
  20                                                  ## data.ident.hit
  20                                                  ## data.ident.hit
  2000 13000 300 12000 7000 0.075 7.5 800 1 30         ## data.ident.ppr
  2000 13000 300 12000 7000 1 7.5 800 1 30             ## data.ident.ppr
  2.5 2.75                                            ## data.ident.scores
  2.5 2.75                                            ## data.ident.scores
  400 600                                              ## data.ident.soi
  400 600                                              ## data.ident.soi
Line 61: Line 63:
  200                                                  ## data.defx.start
  200                                                  ## data.defx.start
  30 45                                                ## data.qual.qtresvalthresh
  30 45                                                ## data.qual.qtresvalthresh
  10                                                   ## data.qual.nbins
  15                                                   ## data.qual.nbins
  20 800                                              ## data.qual.noiselvl
  0.20 6.0                                            ## data.qual.noiselvl
  0.2500                                               ## data.qual.noisewf
  0.3000                                               ## data.qual.noisewf
  150 1500                                            ## data.qual.baslnrrorlvl
  0.15 40                                              ## data.qual.baslnrrorlvl
  0.2000                                               ## data.qual.baslerrwf
  0.1500                                               ## data.qual.baslerrwf
  200 800                                              ## data.qual.respowerlvl
  200 1200                                            ## data.qual.respowerlvl
  0.2500                                               ## data.qual.respowerwf
  0.1500                                               ## data.qual.respowerwf
  5 80                                                ## data.qual.npeakslvl
  14 70                                                ## data.qual.npeakslvl
  0.3000                                               ## data.qual.npeakswf
  0.4000                                               ## data.qual.npeakswf
  2000 13000 7000 0.075 7.5 800 1 30                   ## data.maldi.ppr
  2000 13000 7000 1 7.5 800 1 30                       ## data.maldi.ppr
  2000 700 2000 0.10 5 800 1 99999999                 ## data.lcms1.ppr
  2000 700 2000 1 5 800 1 99999999                     ## data.lcms1.ppr


</tt>
</tt>
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|}
|}
</ul></ul>
</ul></ul>
It is required to restart MicrobeMS to initialize changes made to the ''microbems.opt'' file.
MicrobeMS must be restarted to apply the changes to the ''microbems.opt'' (parameters may have changed).


== Parameters stored in microbems.opt ==
== Parameters stored in ''microbems.opt'' ==


'''General parameters'''
'''General parameters'''
* ''data.DefFile'' - name of the parameter file. Usually 'microbems.opt', Please do not modify!
* ''data.DefFile'' - name of the parameter file. Usually ''microbems.opt'', Please do not modify!
* ''data.defx.start'' - start value (in m/z units) of the m/z vector used by the function defx (modification not recommended)
* ''data.defx.start'' - first value (in m/z units) of the m/z vector used by the function defx (modification not recommended)
* ''data.allwdispdbavspc'' - if set to '''1''': database or average spectra are displayed in the spectra panel, otherwise '''0'''
* ''data.allwdispdbavspc'' - if set to '''1''': database or average spectra are displayed in the spectra panel, otherwise '''0'''
* ''data.usebasintpiktbl'' - if set to '''1''': use baseline-corrected intensities for the generation of peak tables , otherwise '''0'''
* ''data.usebasintpiktbl'' - if set to '''1''': use baseline-corrected intensities for the generation of peak tables, otherwise '''0'''
* ''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
'''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, 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.niv'' - defines the number of segments (intervals) used spectra for baseline correction, 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]]
Line 96: Line 100:
* ''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'''
* ''data.mkdb.threshold'' - defines the minimum required frequency a peak must be present in the individual peak tables
* ''data.mkdb.threshold'' - defines the minimum frequency a peak must be present in the individual peak tables when creating database spectra [''0 &le; data.mkdb.threshold &le; 1'']: peaks are not added to the peak tables of database spectra if their frequency is smaller than ''data.mkdb.threshold''
* ''data.mkdb.fmaxnpks'' - a factor defining how much the number of peaks in the database spectrum may exceed the number of peaks present in individual mass spectra
* ''data.mkdb.fmaxnpks'' - factor defining the maximum number of peaks to be included in the peaklist of the database spectrum [''0 &le; data.mkdb.fmaxnpks &le; 1'']; data.mkdb.fmaxnpks &times; 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]]
* ''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.niv'' - defines the number of intervals (baseline correction), 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'' - useful to narrow the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut|cut]]
Line 108: Line 112:
* ''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  
* ''data.ident.scores'' - log scores thresholds, required for visualization of identification results of ''score ranking lists'' according to the traffic light scheme
* ''data.ident.soi'' - scores thresholds, used for visualization of identification results of ''rank list analyses'' according to the traffic light scheme
* ''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
'''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.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.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.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.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.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. 0.82 and later): http://wiki.microbe-ms.com/uploads/microbems.opt
The text file ''microbems.opt'' can be downloaded here (MicrobeMS v. 0.88 and later): https://wiki.microbe-ms.com/uploads/microbems.opt

Latest revision as of 07:50, 4 April 2025

Introduction

This section describes the format of the parameter file microbems.opt of MicrobeMS v. 0.87 and later.

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 database spectra and in the workflow for microbial identification based on mass spectral libraries and interspectral distances.
The parameter file can be usually found in one of the following directories:

      • Compiled Windows versions of MicrobeMS (MCR required): C:\Users\Public\Documents\Matlab.
      • MicrobeMS installed as a Matlab toolbox (pcode) on Windows operating systems (Windows 7/8/8.1/10/11): root directory of the MicrobeMS toolbox, usually 'C:\Users\WindowsUserName\Documents\Matlab\mass' with WindowsUserName being the user's Windows name.
      • LINUX versions (pcode): microbems.opt must reside in the pcode toolbox directory of MicrobeMS. Type
            >> which mass
            at the Matlab prompt when searching for this directory.

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:

      Content of the file microbems.opt: 

      ###
800                                                  ## data.pre.autoppm
1 -4 5 8 60                                          ## data.pre.basln
21                                                   ## data.pre.smo
5                                                    ## data.pre.redres
2000 13000                                           ## data.pre.cut
microbems.opt                                        ## data.DefFile
#- SMO#- BAS#- NRM                                   ## data.mkdb.seq
21                                                   ## data.mkdb.nsp
1 -4 5 8 60                                          ## data.mkdb.bas
1                                                    ## data.mkdb.nrm
2000 15000                                           ## data.mkdb.cut
1                                                    ## data.mkdb.red
                                                     ## data.mkdb.clb
2000 13000 300 12000 7000 1 7.5 800 1 40             ## data.mkdb.ppr
1                                                    ## data.mkdb.int
0.25                                                 ## data.mkdb.threshold
0.75                                                 ## data.mkdb.fmaxnpks
1                                                    ## data.allwdispdbavspc
1                                                    ## data.usebasintpiktbl
#- SMO#- BAS#- NRM                                   ## data.ident.seq
21                                                   ## data.ident.nsp
1 -4 8 8 60                                          ## data.ident.bas
1                                                    ## data.ident.nrm
2000 15000                                           ## data.ident.cut
1                                                    ## data.ident.red
                                                     ## data.ident.clb
20                                                   ## data.ident.hit
2000 13000 300 12000 7000 1 7.5 800 1 30             ## data.ident.ppr
2.5 2.75                                             ## data.ident.scores
400 600                                              ## data.ident.soi
'2023-Feb-06-full-db-800ppm-40-peaks-0.pkf'          ## data.ident.pkf
'E:\MALDI MO\MALDI DB\Peaklists (pkf)'               ## data.ident.pth
200                                                  ## data.defx.start
30 45                                                ## data.qual.qtresvalthresh
15                                                   ## data.qual.nbins
0.20 6.0                                             ## data.qual.noiselvl
0.3000                                               ## data.qual.noisewf
0.15 40                                              ## data.qual.baslnrrorlvl
0.1500                                               ## data.qual.baslerrwf
200 1200                                             ## data.qual.respowerlvl
0.1500                                               ## data.qual.respowerwf
14 70                                                ## data.qual.npeakslvl
0.4000                                               ## data.qual.npeakswf
2000 13000 7000 1 7.5 800 1 30                       ## data.maldi.ppr
2000 700 2000 1 5 800 1 99999999                     ## data.lcms1.ppr

MicrobeMS must be restarted to apply the changes to the microbems.opt (parameters may have changed).

Parameters stored in microbems.opt

General parameters

  • data.DefFile - name of the parameter file. Usually microbems.opt, Please do not modify!
  • data.defx.start - first value (in m/z units) of the m/z vector used by the function defx (modification not recommended)
  • data.allwdispdbavspc - if set to 1: database or average spectra are displayed in the spectra panel, otherwise 0
  • data.usebasintpiktbl - if set to 1: use baseline-corrected intensities for the generation of peak tables, otherwise 0
  • data.maldi.ppr - parameters used for peak picking of MALDI-ToF mass spectra, see peak detection for details
  • data.lcms1.ppr - not used

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
  • data.mkdb.nsp - the number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, smoothing
  • data.mkdb.bas - defines parameters used for spectral baseline correction, for details see spectral pre-processing, baseline correction
  • data.mkdb.nrm - if set to 1 spectra are normalized otherwise 0, see spectral pre-processing, normalization
  • data.mkdb.cut - useful to narrow the m/z range of mass spectra, see spectral pre-processing, cut
  • data.mkdb.red - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, reduce resolution
  • data.mkdb.clb - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, auto-calibration
  • data.mkdb.ppr - peak detection parameters, see peak detection for details
  • 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.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

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.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.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.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.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.respowerwf - weighting factor of the QT parameter 'resolving power' (default 0.15)

Downloading microbems.opt

The text file microbems.opt can be downloaded here (MicrobeMS v. 0.88 and later): https://wiki.microbe-ms.com/uploads/microbems.opt

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