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

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

• 02-PIA_and_quantKNIME Hub
• basic_peptide_identification_with_inferenceKNIME Hub
• basic_peptide_identification_with_inferenceKNIME Hub
• basic_peptide_identification_with_inference_and_spectral_countingOpenMS
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Show all 9 workflows

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