Description of MicrobeMS' main parameter file 'microbems.opt'

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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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