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required parameter

advanced parameter

+ProteinQuantifierCompute peptide and protein abundances

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ProteinQuantifier'

in Input fileinput file*.featureXML,*.consensusXML

protxml ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.
Information about indistinguishable proteins will be used for protein quantification.input file*.idXML

out Output file for protein abundancesoutput file*.csv

peptide_out Output file for peptide abundancesoutput file*.csv

mzTab_out Export to mzTab.
Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together.output file*.csv

top3 Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)0:∞

averagemedian Averaging method used to compute protein abundances from peptide abundancesmedian,mean,sum

include_allfalse Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)true,false

filter_chargefalse Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;
for proteins, abundances will be computed based only on the most prevalent charge of each peptide.
By default, abundances are summed over all charge states.true,false

ratiosfalse Prints the log2 ratios of the abundance value to the output file. (log_2(x_0/x_0) log_2(x_1/x_0) log_2(x_2/x_0) ....)true,false

ratiosSILACfalse Prints the SILAC log2 ratios for a triple SILAC experiment to the output file. Only performed if three maps are given, otherwise nothing will be seen in the output file. (log_2(heavy/light) log_2(heavy/middle) log_2(middle/light)true,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++consensusAdditional options for consensus maps

normalizefalse Scale peptide abundances so that medians of all samples are equaltrue,false

fix_peptidesfalse Use the same peptides for protein quantification across all samples.
With 'top 0', all peptides that occur in every sample are considered.
Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,
breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!).true,false

+++formatOutput formatting options

separator Character(s) used to separate fields; by default, the 'tab' character is used

quotingdouble Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,
'escape' for quoting with backslash-escaping of embedded quotesnone,double,escape

replacement_ If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing