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

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## Introduction

The file microbems.opt is a simple text file which is read upon initialization of the MicrobeMS program. The microbems.opt file contains some program-wide parameters and parameters required for auto-preprocessing and auto-peak detection from or in raw (original) mass spectra. Auto-preprocessing and auto-peak detection is carried out upon the generation of database spectra and in the microbial identification workflow based on mass spectral libraries and interspectral distances. The file microbems.opt can be usually found in one of the following directories:

• MicrobeMS installed as a Matlab toolbox (pcode), Windows operating system (XP/Vista/W7/W8/W8.1): root directory of the MicrobeMS toolbox, usually 'C:\program files\Matlab\R2014a\toolbox\matlab\mass' with C:\program files\Matlab\R2014a equaling the variable 'matlabroot'. Note that R2014a denotes the Matlab version which is currently used.
• Alternatively, the file microbems.opt can be also stored in the directory C:\users\WindowsUserName\Documents\Matlab with WindowsUserName being the user's Windows name.

## 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 opened file microbems.opt shows the following content:

 Content of the file microbems.opt: ```### microbems.opt                              ## data.DefFile #- SMO#- BAS#- NRM                         ## data.mkdb.seq 21                                         ## data.mkdb.nsp 80                                         ## data.mkdb.niv 1                                          ## data.mkdb.nrm 1                                          ## data.mkdb.clb 2000 12000 600 12000 2000 0.2 7 1000 1 30  ## data.mkdb.ppr 1                                          ## data.mkdb.int 0.25                                       ## data.mkdb.threshold 1.6                                        ## data.mkdb.fmaxnpks 1                                          ## data.allwdispdbavspc 1                                          ## data.usebasintpiktbl #- SMO#- BAS#- NRM                         ## data.ident.seq 21                                         ## data.ident.nsp 80                                         ## data.ident.niv 1                                          ## data.ident.nrm 1                                          ## data.ident.clb 2000 12000 600 12000 2000 0.2 7 1000 1 30  ## data.ident.ppr 'name_of_peaklist_file.pkf'                ## data.ident.pkf 'S:\OE\ZBS6_RL\databases\maldi\peaklists'  ## data.ident.pth 200                                        ## data.defx.start ```

It is required to restart MicrobeMS to initialize changes made to the microbems.opt file.

## Parameters stored in microbems.opt

General parameters

• data.DefFile - name of the parameter file. 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.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 - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, smoothing
• data.mkdb.niv - defines the number of intervals (baseline correction), 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.clb - autocalibration parameters (not used in version 0.77), 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 in the single 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.niv - defines the number of intervals (baseline correction), 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.clb - autocalibration parameters (not used in version 0.77), see spectral pre-processing, auto-calibration
• data.ident.ppr - peak detection parameters, see peak detection for details
• data.ident.pkf - name of the peak list file used for identification based on mass spectral libraries and interspectral distances
• data.ident.pth - path to the peak list file used for identification based on mass spectral libraries and interspectral distances

## Downloading microbems.opt

The text file microbems.opt can be downloaded here: http://wiki.microbe-ms.com/microbems.opt