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 (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.
- LINUX versions (pcode): microbems.opt must reside in the pcode toolbox directory of MicrobeMS. Type
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 0.075 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 0.075 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
10 ## data.qual.nbins
20 800 ## data.qual.noiselvl
0.2500 ## data.qual.noisewf
150 1500 ## data.qual.baslnrrorlvl
0.2000 ## data.qual.baslerrwf
200 800 ## data.qual.respowerlvl
0.2500 ## data.qual.respowerwf
5 80 ## data.qual.npeakslvl
0.3000 ## data.qual.npeakswf
2000 13000 7000 0.075 7.5 800 1 30 ## data.maldi.ppr
2000 700 2000 0.10 5 800 1 99999999 ## data.lcms1.ppr
|
MicrobeMS must be restarted to apply the changes to the microbems.opt.
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, 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 required frequency a peak must be present in the individual peak tables
- 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
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
- data.ident.nsp - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, smoothing
- data.ident.bas - defines parameters used for spectral baseline correction, for details see spectral pre-processing, baseline correction
- data.ident.nrm - if set to 1 spectra are normalized otherwise 0, see spectral pre-processing, normalization
- data.ident.cut - useful to narrow the m/z range of mass spectra, see spectral pre-processing, cut
- data.ident.red - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, reduce resolution
- data.ident.clb - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, 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
- data.ident.ppr - peak detection parameters, see 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
- data.ident.pth - path to the peak list file indicated, see 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: 10
- data.qual.noiselvl - noise level settings, in the default settings the noise parameter may vary between 20 (almost perfect, score of 100) and 800 (failed, score of 0)
- data.qual.noisewf - weighting factor of the QT parameter 'noise level' (default 0.25)
- data.qual.baslnrrorlvl - baseline error settings, as per default settings the baseline parameter may vary between 150 (almost perfect, score of 100) and 1500 (failed, score of 0)
- data.qual.baslerrwf - weighting factor of the QT parameter 'baseline' level (default 0.20)
- data.qual.respowerlvl - resolving power settings, the parameter may vary between 200 (very poor, score of 0) and 800 (excellent, score of 100)
- data.qual.respowerwf - weighting factor of the QT parameter 'resolving power' (default 0.25)
- data.qual.npeakslvl - number of peaks, in the default settings this parameter may vary between 5 (very poor, score of 0) and 80 (excellent, score of 100)
- data.qual.npeakswf - weighting factor of the QT parameter 'number of peaks' (default 0.30)
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