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

Introduction

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 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, Notepad++, Nano, etc. The following table shows an example of the contents of microbems.opt:

Content of the file microbems.opt:

### 800 ## data.pre.autoppm 1 -2 7 8 60 ## data.pre.basln 21 ## data.pre.smo 5 ## data.pre.redres 2000 15000 ## data.pre.cut microbems.opt ## data.DefFile #- SMO#- BAS#- NRM ## data.mkdb.seq 21 ## data.mkdb.nsp 1 -2 7 8 60 ## data.mkdb.bas 1 ## data.mkdb.nrm 2000 15000 ## data.mkdb.cut 1 ## data.mkdb.red ## data.mkdb.clb 3000 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 -2 7 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 3000 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 #- SMO#- BAS#- NRM ## data.bdal.seq 21 ## data.bdal.nsp 1 -2 7 8 60 ## data.bdal.bas 1 ## data.bdal.nrm 2000 15000 ## data.bdal.cut 1 ## data.bdal.red ## data.bdal.clb 3000 15000 300 12000 7000 1 10 800 1 100 ## data.bdal.ppr 2.0 2.3 ## data.bdal.scores 150 400 ## data.bdal.soi 600 ## data.bdal.ppm 30 45 ## data.qual.qtresvalthresh 15 ## data.qual.nbins 0.4 3.5 ## data.qual.noiselvl 0.30 ## data.qual.noisewf 1 45 ## data.qual.baslnrrorlvl 0.15 ## data.qual.baslerrwf 8 50 ## data.qual.npeakslvl 0.40 ## data.qual.npeakswf 250 1100 ## data.qual.respowerlvl 0.15 ## data.qual.respowerwf 3000 13000 300 12000 7000 1 7.5 800 0 30 ## data.qual.ppr 3000 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 made to 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 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 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

• 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 - narrows 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

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

• 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 0.40 (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.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.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.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)

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