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

Introduction

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

• Compiled Windows versions of MicrobeMS (MCR required): The file microbems.opt can usually be found in the directory 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 >> which mass at the Matlab prompt when searching for this directory.

Content 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 file.

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

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 - log scores thresholds, required 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

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