Below is a sample configuration file. Although it is not necessary to specify every parameter, doing so is highly recommended so that you know explicitly the parameters being used. For ease of reading, comments and notes are allowed after a # character. Feel free to include your own comments when creating and using your configuration files.
# Hardklor parameter file
# Version 2.18, Release Date: Jan 26 2015
# Please see online documentation for detailed explanations:
# https://code.google.com/p/hardklor/wiki/Documentation
# All parameters are separated from their values by an equals sign ('=')
# Anything after a '#' will be ignored for the remainder of the line.
# All data files (including paths if necessary) to be analyzed are discussed below.
# Parameters used to described the data being input to Hardklor
instrument = Orbitrap #Values are: FTICR, Orbitrap, TOF, QIT
resolution = 55000 #Resolution at 400 m/z
centroided = 0 #0=no, 1=yes
# Parameters used in preprocessing spectra prior to analysis
ms_level = 1 #1=MS1, 2=MS2, 3=MS3, 0=all
scan_range_min = 0 #ignore any spectra lower than this number, 0=off
scan_range_max = 0 #ignore any spectra higher than this number, 0=off
signal_to_noise = 0 #set signal-to-noise ratio, 0=off
sn_window = 250.0 #size in m/z for computing localized noise level in a
# spectrum.
static_sn = 0 #0=off, 1=on. Apply lowest localized noise level to
# entire spectrum.
boxcar_averaging = 0 #0=off, or specify number of scans to average together,
# use odd numbers only
boxcar_filter = 0 #0=off, when using boxcar_averaging, only keep peaks
# seen in this number of scans currently being
# averaged together. When on, signal_to_noise is not
# used.
boxcar_filter_ppm = 5 #Tolerance in ppm for matching peaks across spectra in
# boxcar_filter
mz_min = 0 #Lower bound of spectrum m/z range to analyze, 0=off
mz_max = 0 #Upper bound of spectrum m/z range to analyze, 0=off
smooth = 0 #Savitzky-Golay smoothing of peaks data. 0=off
# Not recommended for high resolution data.
# Parameters used to customize the Hardklor analysis. Some of these parameters will drastically
# affect the analysis speed and results. Please consult the documentation and choose carefully!
algorithm = Version2 #Algorithms include: Basic, Version1, Version2
charge_algorithm = Quick #Preferred method for feature charge identification.
# Values are: Quick, FFT, Patterson, Senko, None
# If None is set, all charge states are assumed, slowing Hardklor
charge_min = 1 #Lowest charge state allowed in the analysis.
charge_max = 5 #Highest charge state allowed in the analysis.
correlation = 0.95 #Correlation threshold to accept a peptide feature.
averagine_mod = 0 #Formula containing modifications to the averagine model.
# Read documentation carefully before using! 0=off & clears all existing modifications.
mz_window = 5.25 #Breaks spectrum into windows not larger than this value for Version1 algorithm.
sensitivity = 3 #Values are 0 (lowest) to 3 (highest). Increasing sensitivity
# identifies more features near the noise where the isotope distribution
# may not be fully visible. However, these features are also more
# likely to be false.
depth = 2 #Depth of combinatorial analysis. This is the maximum number of overlapping
# features allowed in any mz_window. Each increase requires exponential
# computation. In other words, keep this as low as necessary!!!
max_features = 15 #Maximum number of potential features in an mz_window to combinatorially solve.
# Setting this too high results in wasted computation time trying to mix-and-match
# highly improbable features.
# Parameters used to customize the Hardklor output
distribution_area = 0 #Report sum of distribution peaks instead of highest peak only. 0=off, 1=on
xml = 0 #Output results as XML. 0=off, 1=on
# Below this point is where files to be analyzed should go. They should be contain both
# the input file name and the output file name. Each file to be analyzed should begin
# on a new line. By convention Hardklor output should have this extension: .hk
# Example:
#YourData.mzXML YourData.hk