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ProteinQuantifier (version 2.8+galaxy0)

Input file:

select consensusxml,featurexml,idxml data sets(s)

Protein inference results for the identification runs that were used to annotate the input:

(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)

input file containing the experimental design:

select tabular data sets(s)

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

Averaging method used to compute protein abundances from peptide abundances:

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

Distinguish between fraction and charge states of a peptide:

For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states

Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities:

(Only works with an idXML file given as protein_groups parameter)

Add the log2 ratios of the abundance values to the output:

Format: log_2(x_0/x_0) log_2(x_1/x_0) log_2(x_2/x_0)

Add the log2 ratios for a triple SILAC experiment to the output:

Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) log_2(heavy/middle) log_2(middle/light)

Additional options for consensus maps (and identification results comprising multiple runs)s

Additional options for consensus maps (and identification results comprising multiple runs) 0

Output formatting options

Output formatting options 0

Advanced Options

Advanced Options 0

Optional outputs: