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ProteinQuantifier

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Compute peptide and protein abundances

Web Documentation for ProteinQuantifier

Options

version
Version of the tool that generated this parameters file.
top
Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)
average
Averaging method used to compute protein abundances from peptide abundances
include_all
Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)
filter_charge
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.
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
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 '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!).
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

Input file [featureXML,consensusXML,idXML]
Protein inference results for the identification runs that were used to annotate the input (e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).#br#Information about indistinguishable proteins will be used for protein quantification. [idXML,opt.]

Output Ports

Output file for protein abundances [csv,Inactive]
Output file for peptide abundances [csv,Inactive]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

KNIME 3.7
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