/
ground_truth.conf
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/
ground_truth.conf
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############################################################################
## GroundTruthSimulator parameter file
## Version 1.0.0, Release Date: Sept 20, 2015
## See README.txt for details
############################################################################
## All parameters are separated from their values by an equals sign ('=')
## '#' are comments and everything after them is ignored until the next line
############################################################################
############################################################################
## Modifications
## Each line represents a different modification
## -n = Full name of modifications
## -b = Abbreviation for modification. This will be used when writing the
## sequence of a peptide, e.g. PEPpTIDE, AcarCDEFG
## -r = List of residues the modification can be on. "n" is for N-terminal
## modifications and "c" is for C-terminal modifications
## -p = Probability that a residue will ever have this modification.
## For example, -p1 would mean every residue defined by "-r" will have
## at least some copies with this modification. -p0.5 will result in a
## random 50% of residues never having this modification.
## -a = Relative abundance of the modification on a particular residue. For
## those residues randomly chosen to have this modification, how many
## copies will exist with it? For example, -a1 would mean that if the
## residue was selected to have this modification, then all copies of
## this residue will have the modification. -a0.9999 would result in
## 0.0001 percent of the copies to not have the modification. -p1 -a1
## would create a classic "static" modification. Low aboundance PTMs
## such as ubiquitination should have a low value for this parameter
## -m = Molecular formula for this modification. Format is the standard
## abbreviation used for the element followed by the number of the
## element. Each element and count combination is separated by a comma.
## Negative numbers are allowed.
## -e = Bind energy of the modification. This affects the retention time of
## peptides having this modification. Retention time is predicting with
## the BioLCCC library. Please refer to their documentation for how to
## set this: http://pythonhosted.org/pyteomics.biolccc/
## Phosphorylation bind energy was taken from their document. Depending
## on the residue, the bind energy is different, which is why the
## modification is split into 3 separate lines. If you don't know what
## the value of this parameter should be, try a guess! Just don't make
## it too big. Positive numbers increase retention time. 0 Has no effect.
## --blocks_cleavage = This PTM will inhibit digestion.
## Excluding this parameter means the PTM does not block
## cleavage
## ** NOT IMPLEMENTED YET **
## --stackable = This PTM can stack with other PTMs.
## Excluding this parameter means the PTM does not stack
## ** NOT IMPLEMENTED YET **
## --post_digestion = This PTM should be added after in silico digestion
## Excluding this parameter means the PTM is present pre
## digestion
## ** NOT IMPLEMENTED YET **
############################################################################
PTM= -nCarbamidomethyl -bcar -rC -p1 -a0.9999 -mH3,C2,N1,O1 -e0.77
#PTM= -nPhosphorylationS -bp -rS -p0.1 -a0.01 -mH1,O3,P1 -e-0.45
#PTM= -nPhosphorylationT -bp -rT -p0.1 -a0.01 -mH1,O3,P1 -e-0.74
#PTM= -nPhosphorylationY -bp -rY -p0.1 -a0.01 -mH1,O3,P1 -e-1.32
#PTM= -nProteinAcetylation -bAc- -rn -p0.5 -a0.1 -mC2,H2,O1 -e0.0
#PTM= -nAcetylation -bac -rK -p0.01 -a0.002 -mC2,H2,O1 -e0.1 --blocks_cleavage
#PTM= -nGlyGly -bubi -rK -p0.05 -a0.001 -mH6,C4,N2,O2 -e0.05 --blocks_cleavage
#PTM= -nDeamidation -bd -rNQ -p0.2 -a0.01 -mH-1,N-1,O1 -e-0.1
PTM= -nOxidation -box -rM -p0.5 -a0.05 -mO1 -e1.8215
#PTM= -nLys6 -bl6 -rK -p1 -a0.99 -mn6 -e0 --stackable
#PTM= -nPropionyl -bprop -rK -p1 -a0.99 -mH4,C3,O1 -e4.0 --post_digestion
############################################################################
## Enzymes
## Each line represents a different enzyme
## -n = Name of the enzyme
## -r = List of residues this enzyme should cleaved at. '*' is a wild card
## and means all residues can be cut. Useful to model non-specific
## cleavage
## -p = Relative frequency of cleavage at this residue. -p1 would result in
## no missed cleavages.
## -t = Terminus of cleavage. 'C' = C-terminus, 'N' = N-terminus
## -b = Residues that block cleavage. ** NOT IMPLEMENTED YET **
############################################################################
Enzyme= -nTrypsinR -rR -p0.99 -tC -bP
Enzyme= -nTrypsinK -rK -p0.95 -tC -bP
Enzyme= -nRandom -r* -p0.001 -tC
############################################################################
## BioLCCC parameters for liquid chromatography retention time prediction
## Please refer to their documentation for details:
## http://pythonhosted.org/pyteomics.biolccc/
############################################################################
column_length= 150 # length in mm
column_diameter= .075 # diameter in mm
column_pore_size= 100 # pore size in angstroms
second_solvent_concentration_a= 2.0 # Percentage * 100
second_solvent_concentration_b= 80.0 # Percentage * 100
gradient_percent_b_start= 0.0 # Percentage * 100
gradient_percent_b_end= 50.0 # Percentage * 100
gradient_duration= 185.0 # Time in minutes
gradient_flow_rate= 0.00025 # ml/min
############################################################################
## Elution profile shape parameters
## A exponential-Gaussian hybrid function (EGH) is used to model the shape
## Please refer to "A hybrid of exponential and gaussian functions as a
## simple model of asymmetric chromatographic peaks" by Kevin Lan and James
## W. Jorgenson, Journal of Chromatography, Part A, 915, 1-13 (2001).
############################################################################
elution_sigma=6 # width of elution profile = ~6 x elution_sigma seconds
elution_tau=4 # influences amount of tailing, 0 = gaussian shape
############################################################################
## Miscellaneous
############################################################################
max_mass= 10000 # amu
max_mz= 3000 #
min_mz= 300 #
prune_threshold= 1e4 # The minimum abundance for any ion to be
# included in the simulation. it is used for
# filtering purposes. Decreasing this will
# increase run-time and file sizes. If you used
# the recommended abundances for proteins then
# this is probably a good number. Ions below
# this threshold are very unlikely to be
# observed in a typical MS1 scan.