Sample Configuration File

# Kojak version 2.0.0alpha16 parameter file
# Please see online documentation at:
# http://www.kojak-ms.org/param

# All parameters are separated from their values by an equals sign ('=')
# Anything after a '#' will be ignored for the remainder of the line.

#
# Computational resources
#
threads     =   0  #0=all threads, or specify exact number. Use -1 for all but 1 thread, etc.

#
# Data input files: include full path if not in current working directory
#
database = yourDB.fasta
export_percolator = 1
export_pepXML = 1
export_mzID = 1
MS_data_file = yourData.mzML
percolator_version = 3.04
results_path = .

#
# Parameters used to described the data being input to Kojak
#
enrichment = 0       	#Values between 0 and 1 to describe 18O APE.
                        #For example, 0.25 equals 25 APE.
instrument = 0          #Values are: 0=Orbitrap, 1=FTICR (such as Thermo LTQ-FT)
MS1_centroid = 1        #0=no, 1=yes
MS2_centroid = 1        #0=no, 1=yes
MS1_resolution = 50000  #Resolution at 400 m/z, value ignored if data are
                        #already centroided
MS2_resolution = 50000  #Resolution at 400 m/z, value ignored if data are
                        #already centroided
							
#
# Cross-link and mono-link masses allowed. May have more than one of each parameter.
#
# Format for cross_link is [amino acids] [amino acids] [mass mod] [identifier]
# Format for mono_link is [amino acids] [mass mod]
# One or more amino acids (uppercase only!!) can be specified for each linkage moiety
# Use lowercase 'n' or 'c' to indicate protein N-terminus or C-terminus
#
cross_link = nK  nK  138.0680742 DSS
mono_link = nK 156.0786442515      #DSS_H2O_monolink
mono_link = nK 155.0946286667      #DSS_NH2_monolink

#
# Fixed modifications. Add as many as necessary.
#
fixed_modification = C 57.02146
fixed_modification_protC = 0
fixed_modification_protN = 0

#
# Differential modifications. Add as many as necessary. Uppercase only for amino acids!
# n = peptide N-terminus, c = peptide C-terminus
#
# If more than one modification is possible for an amino acid, 
# list all modifications on separate lines
#
modification = M 15.9949
modification_protC = 0
modification_protN = 0
diff_mods_on_xl = 0
max_mods_per_peptide = 2
mono_links_on_xl = 0

#
# Digestion enzyme rules.
#
# See http://www.kojak-ms.org/param/enzyme.html
#
enzyme = [KR]|{P} Trypsin

#
# Scoring algorithm parameters
#
# fragment_bin_offset and fragment_bin_size influence algorithm precision and memory usage.
# They should be set appropriately for the data analyzed.
# For ion trap ms/ms:  1.0005 size, 0.4 offset
# For high res ms/ms:    0.01 size, 0.0 offset
#
fragment_bin_offset = 0.0  #between 0.0 and 1.0
fragment_bin_size = 0.01   #in Thomsons
ion_series_A = 0
ion_series_B = 1
ion_series_C = 0
ion_series_X = 0
ion_series_Y = 1
ion_series_Z = 0		   #Z-dot values are used

#
# Additional parameters used in Kojak analysis
#
decoy_filter = REVERSE 0   #First value specifies identifier for all decoys in the database.
                           #Second value requests Kojak to generate the decoys on-the-fly: 0=off, 1=on
e_value_depth = 5000       #minimum number of values required when computing e-values. Default=5000
isotope_error = 2          #account for errors in precursor peak identification.
                           #Searches this number of isotope peak offsets.
                           #Values are 0,1,2, or 3.
max_miscleavages = 2       #number of missed trypsin cleavages allowed
max_peptide_mass = 6000.0  #largest allowed peptide mass in Daltons
min_peptide_mass = 600.0   #lowest allowed peptide mass in Daltons
min_peptide_score = 0.5    #minimim individual peptide score to be considered for second pass analysis.
min_spectrum_peaks = 20    #skip MS/MS spectra with fewer than this number of peaks.
max_spectrum_peaks = 0     #top N peaks to use during analysis. 0 uses all peaks.
precursor_refinement = 1   #0=off, 1=on. See online documentation for details.
ppm_tolerance_pre = 8      #mass tolerance on precursor when searching
prefer_precursor_pred = 2  #prefer precursor mono mass predicted by
                           #instrument software.
                           #  0 = ignore previous predictions
                           #  1 = use only previous predictions
                           #  2 = supplement predictions with additional analysis
spectrum_processing = 1    #0=no, 1=yes. See online documentation for details.
top_count = 10             #number of top scoring alpha peptides to maintain after first pass.
                           #not recommended to use below 5 or more than 50.
truncate_prot_names = 0    #Max protein name characters to export, 0=off