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Hardklor.conf
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# Hardkor parameter file
# One day there may be online documentation for detailed explanations:
# http://proteome.gs.washington.edu/software/hardklor
# http://code.google.com/p/hardklor
# 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.
# Hardklor uses two data files. If these are stored elsewhere, please alter the path
# to the correct location.
isotope_data = C:\Hardklor\ISOTOPE.DAT
hardklor_data = C:\Hardklor\Hardklor.dat
# 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 #Sets lower bound of spectrum m/z range to analyze, 0=off
mz_max = 0 #Sets upper bound of spectrum m/z range to analyze, 0=off
smooth = 0 #Peforms 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 listed 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