View source for Description of MicrobeMS' main parameter file 'microbems.opt'

== Introduction ==

'''Important notice''': With MicrobeMS v. 0.82 the format of the parameter file ''microbems.opt'' has changed!

The file ''microbems.opt'' is a simple text file which is read upon initialization by MicrobeMS. The file ''microbems.opt'' contains a number of program-wide 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 [[Create database spectra|database spectra]] and in the [[Microbial Identification based on Mass Spectral Libraries and Interspectral Distances|workflow for microbial identification based on mass spectral libraries and interspectral distances]]. <br>  
The file ''microbems.opt'' can be usually found in one of the following directories: 

<ul><ul>

* MicrobeMS installed as a Matlab toolbox (pcode), Windows operating system (XP/Vista/W7/W8/W8.1/W10): 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 the string 'R2014a' denotes the Matlab version which is actually 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 (compiled Windows versions of MicrobeMS).

* LINUX version (Debian): the file ''microbems.opt'' must reside in the pcode toolbox directory of MicrobeMS. Type ' >> which mass ' at the Matlab prompt when searching for this directory.

</ul></ul>

== 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':

<ul><ul>
{| class="wikitable" width=650
|width=800| '''Content of the file''' '''''microbems.opt''''':
|-
|
<tt>
 ###
 microbems.opt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.DefFile
 #- SMO#- BAS#- NRM#- CUT#- RED &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.mkdb.seq
 21 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.mkdb.nsp
 80 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.mkdb.niv
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.mkdb.nrm
 2000 15000&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; ## data.mkdb.cut
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.mkdb.red
 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.mkdb.clb
 2000 12000 600 12000 2000 0.2 7 1000 1 30 &nbsp;## data.mkdb.ppr
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.mkdb.int
 0.25 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.mkdb.threshold
 1.6 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.mkdb.fmaxnpks
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.allwdispdbavspc
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.usebasintpiktbl
 #- SMO#- BAS#- NRM#- CUT#- RED &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.ident.seq
 21 &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.nsp
 80 &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.niv
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.nrm
 2000 15000&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; ## data.ident.cut
 1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.red
 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.clb
 20 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ## data.ident.hit
 2000 12000 600 12000 2000 0.2 7 1000 1 30 &nbsp;## data.ident.ppr
 'name_of_peaklist_file.pkf' &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.ident.pkf
 'S:\OE\ZBS6_RL\databases\maldi\peaklists' &nbsp;## data.ident.pth
 200 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;## data.defx.start
</tt>
|-
|}
</ul></ul>
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. Usually 'microbems.opt', Please 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#|spectral pre-processing]]
* ''data.mkdb.nsp'' - the number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral Pre-processing#Smoothing|smoothing]]
* ''data.mkdb.niv'' - defines the number of segments (intervals) used spectra for baseline correction, see spectral pre-processing, [[Spectral Pre-processing#Baseline correction|baseline correction]]
* ''data.mkdb.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization|normalization]]
* ''data.mkdb.cut'' - useful to narrow the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut|cut]]
* ''data.mkdb.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Reduce_resolution|reduce resolution]]
* ''data.mkdb.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral Pre-processing#Auto-calibration|auto-calibration]]
* ''data.mkdb.ppr'' - peak detection parameters, see  [[Peak Detection|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#|spectral pre-processing]]
* ''data.ident.nsp'' - defines number of smoothing points (Savitzky-Golay smoothing), see spectral pre-processing, [[Spectral Pre-processing#Smoothing|smoothing]]
* ''data.ident.niv'' - defines the number of intervals (baseline correction), see spectral pre-processing, [[Spectral Pre-processing#Baseline correction|baseline correction]]
* ''data.ident.nrm'' - if set to '''1''' spectra are normalized otherwise '''0''', see spectral pre-processing, [[Spectral Pre-processing#Normalization|normalization]]
* ''data.ident.cut'' - useful to narrow the m/z range of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Cut|cut]]
* ''data.ident.red'' - factor to reduce the effective spectral resolution of mass spectra, see spectral pre-processing, [[Spectral Pre-processing#Reduce_resolution|reduce resolution]]
* ''data.ident.clb'' - autocalibration parameters (not used before MicrobeMS version 0.82), see spectral pre-processing, [[Spectral Pre-processing#Auto-calibration|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|Microbial identification based on mass spectral libraries and interspectral distances]]
* ''data.ident.ppr'' - peak detection parameters, see  [[Peak Detection|peak detection]] for details 
* ''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|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|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