ProteinQuantifier

Compute peptide and protein abundances

Web Documentation for ProteinQuantifier

Options

version
Version of the tool that generated this parameters file.
method
- top - quantify based on three most abundant peptides (number can be changed in 'top'). - iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!
best_charge_and_fraction
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.
greedy_group_resolution
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).
ratios
Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) ...
ratiosSILAC
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) <sep> log_2(heavy/middle) <sep> log_2(middle/light)
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
N
Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)
aggregate
Aggregation method used to compute protein abundances from peptide abundances
include_all
Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)
normalize
Scale peptide abundances so that medians of all samples are equal
fix_peptides
Use the same peptides for protein quantification across all samples. With 'N 0',all peptides that occur in every sample are considered. Otherwise ('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!).
separator
Character(s) used to separate fields; by default, the 'tab' character is used
quoting
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 quotes
replacement
If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing

Input Ports

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Input file [featureXML,consensusXML,idXML]
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Protein inference results for the identification runs that were used to annotate the input (e.g. via the ProteinInference tool).#br#Information about indistinguishable proteins will be used for protein quantification. [idXML,opt.]
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input file containing the experimental design [tsv,opt.]

Output Ports

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Output file for protein abundances [csv]
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Output file for peptide abundances [csv]
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Output file (mzTab) [mzTab]

Views

ProteinQuantifier Std Output
The text sent to standard out during the execution of ProteinQuantifier.
ProteinQuantifier Error Output
The text sent to standard error during the execution of ProteinQuantifier. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

Links

Developers

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