IsobaricAnalyzer

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. Setting to "auto" uses HCD and HCID spectra. 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, 132N, 132C, 133N, 133C, 134N).
correction_matrix: Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 16 entries (rows), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading.
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.
channel_134C_description: Description for the content of the 134C channel.
channel_135N_description: Description for the content of the 135N channel.
reference_channel: The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N).
correction_matrix: Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 18 entries (rows), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading.
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

: input raw/picked data file [mzML]

Output Ports

: output consensusXML file with quantitative information [consensusXML]

Popular Predecessors

Popular Successors

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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.)

Workflows

Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.4

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.2.0.202411141610

On NodePit since: 2024-12-06

Last update: 2024-12-21

KNIME versions: v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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