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IsobaricAnalyzer

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Calculates isobaric quantitative values for peptides

Web Documentation for IsobaricAnalyzer

Options

version
Version of the tool that generated this parameters file.
type
Isobaric Quantitation method used in the experiment.
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)
select_activation
Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering.
reporter_mass_shift
Allowed shift (left to right) in Th from the expected position.
min_precursor_intensity
Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation.
keep_unannotated_precursor
Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.
min_reporter_intensity
Minimum intensity of the individual reporter ions to be extracted.
discard_low_intensity_quantifications
Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'.
min_precursor_purity
Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor.
precursor_isotope_deviation
Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.
purity_interpolation
If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan. If set to false, only the precursor scan will be used.
channel_114_description
Description for the content of the 114 channel.
channel_115_description
Description for the content of the 115 channel.
channel_116_description
Description for the content of the 116 channel.
channel_117_description
Description for the content of the 117 channel.
reference_channel
Number of the reference channel (114-117).
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'
channel_113_description
Description for the content of the 113 channel.
channel_114_description
Description for the content of the 114 channel.
channel_115_description
Description for the content of the 115 channel.
channel_116_description
Description for the content of the 116 channel.
channel_117_description
Description for the content of the 117 channel.
channel_118_description
Description for the content of the 118 channel.
channel_119_description
Description for the content of the 119 channel.
channel_121_description
Description for the content of the 121 channel.
reference_channel
Number of the reference channel (113-121). Please note that 120 is not valid.
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'
isotope_correction
Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results.
normalization
Enable normalization of channel intensities with respect to the reference channel. The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!
channel_126_description
Description for the content of the 126 channel.
channel_127N_description
Description for the content of the 127N channel.
channel_127C_description
Description for the content of the 127C channel.
channel_128N_description
Description for the content of the 128N channel.
channel_128C_description
Description for the content of the 128C channel.
channel_129N_description
Description for the content of the 129N channel.
channel_129C_description
Description for the content of the 129C channel.
channel_130N_description
Description for the content of the 130N channel.
channel_130C_description
Description for the content of the 130C channel.
channel_131_description
Description for the content of the 131 channel.
reference_channel
The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131).
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'
channel_126_description
Description for the content of the 126 channel.
channel_127N_description
Description for the content of the 127N channel.
channel_127C_description
Description for the content of the 127C channel.
channel_128N_description
Description for the content of the 128N channel.
channel_128C_description
Description for the content of the 128C channel.
channel_129N_description
Description for the content of the 129N channel.
channel_129C_description
Description for the content of the 129C channel.
channel_130N_description
Description for the content of the 130N channel.
channel_130C_description
Description for the content of the 130C channel.
channel_131N_description
Description for the content of the 131N channel.
channel_131C_description
Description for the content of the 131C channel.
reference_channel
The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C).
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'
channel_126_description
Description for the content of the 126 channel.
channel_127N_description
Description for the content of the 127N channel.
channel_127C_description
Description for the content of the 127C channel.
channel_128N_description
Description for the content of the 128N channel.
channel_128C_description
Description for the content of the 128C channel.
channel_129N_description
Description for the content of the 129N channel.
channel_129C_description
Description for the content of the 129C channel.
channel_130N_description
Description for the content of the 130N channel.
channel_130C_description
Description for the content of the 130C channel.
channel_131N_description
Description for the content of the 131N channel.
channel_131C_description
Description for the content of the 131C channel.
channel_132N_description
Description for the content of the 132N channel.
channel_132C_description
Description for the content of the 132C channel.
channel_133N_description
Description for the content of the 133N channel.
channel_133C_description
Description for the content of the 133C channel.
channel_134N_description
Description for the content of the 134N channel.
reference_channel
The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C).
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'
channel_126_description
Description for the content of the 126 channel.
channel_127_description
Description for the content of the 127 channel.
channel_128_description
Description for the content of the 128 channel.
channel_129_description
Description for the content of the 129 channel.
channel_130_description
Description for the content of the 130 channel.
channel_131_description
Description for the content of the 131 channel.
reference_channel
Number of the reference channel (126-131).
correction_matrix
Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

Input Ports

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input raw/picked data file [mzML]

Output Ports

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output consensusXML file with quantitative information [consensusXML]

Views

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

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Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.3

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