Selecting this check box will result in generation of log file,

  which for each spectrum records the results of the cleaning

  procedure.

  This file is saved in the ..\cleaned\ directory.

  This edit box displays the input data files to be cleaned.

  Either type in the path name of a single file, or click the

  browse button to select file(s) from an open file dialog box.

  Supported data formats are:

       -    Sequest files (*.dta), single spectra

       -    Mascot generic files  (*.mgf), multiple spectra

  This edit box displays the directory into which the cleaned  

  spectra will be saved. By default, the program creates

  a  ..\cleaned\  directory within the directory chosen for the

  input data files.

  Alternatively type in the path name of the directory or click the

  browse button to select a directory from an open directory

  dialog box.

  The program creates cleaned files in the same format (*.dta

  or  *.mgf) as the input data file.

  The name of the cleaned file is the same as the input data

  file, with an additional "_c".

  If selected, the program detects multi-charged isotope peak

  clusters according to the chosen Deconvolution threshold.

  These are then transformed into a single monoisotopic peak.

  All other signals from the cluster are deleted.

  If selected, the program detects singly-charged isotope peak

  clusters according to the chosen Deisotoping threshold.

  These are then transformed into a single monoisotopic peak.

  All other signals from the cluster are deleted.

  If selected, the program removes random noise from the  

  spectrum according to the Random noise threshold.

  Determines bad spectra handling.

  Selecting the first option will leave spectra designated as

  "bad" in the "cleaned" output file. Using this option doesn't

  separate bad spectra from remaining files.

  Selecting the second option creates two sets of output file(s):

  cleaned files (minus the bad spectra), and bad spectra files,

  which are saved in a new directory ..\badspectra\,  within the

  ..\cleaned\ directory.

  The name of the bad spectra file is the same as the input

  data file, with an additional "_bad_c".

  Selecting the third option deletes the bad spectra from the

  output files.

  Clicking this button opens and closes a form allowing user to

  change the internal parameters.

  Clicking this button invokes this document.

  Resets the internal parameters to their default values.

  If selected, the program merges together peaks that are

  closer than the Least Peaks Spacing value.

  Specifies the least allowed spacing between peaks for the  

  Merge peaks algorithm of the program.

  Specifies how many signals are taken for median filtering of

  the power spectrum.

  Specifies the deisotoping filter width.

  Specifies the maximum allowed frequency of the power

  spectrum.

  Starts the cleaning procedure.

  Closes the dialog box and quits the program.

  This mode is used to find the highest possible number of bad

  spectra and reduce the amount of data as much as possible.

  Although some spectra are bad, they can still be interpreted

  by a database search program. With this option, removal of

  bad spectra can lead to a lower sequence coverage, but

  a higher confidence in the interpretation.

  Using this option, fewer bad spectra will be identified.

  This mode is used if a high sequence coverage is more

  important than data reduction.

  The deisotoping procedure reduces the intensity of the

  potential isotope peaks. If the decrease in intensity is

  greater than this threshold value, the intensity of the peak will

  be set to zero.

  The deconvolution procedure detects multi-charged peaks if

  the correlation coefficient is higher than this value.

  This is the stop frequency for the low pass filter used for

  random noise removal.

  This filter reduces the intensity of random noise peaks. If  

  the decrease in intensity is greater than this value, the

  intensity is set to zero.

  Specifies the length of the sequence tag.

  Mass tolerance taken into account during the sequence tag determination.