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MetaProSIP

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

Performs proteinSIP on peptide features for elemental flux analysis.

Web Documentation for MetaProSIP

Options

version
Version of the tool that generated this parameters file.
mz_tolerance_ppm
Tolerance in ppm
rt_tolerance_s
Rolerance window around feature rt for XIC extraction
intensity_threshold
Intensity threshold to collect peaks in the MS1 spectrum.
correlation_threshold
Correlation threshold for reporting a RIA
xic_threshold
Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak. If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present.
decomposition_threshold
Minimum R-squared of decomposition that must be achieved for a peptide to be reported.
weight_merge_window
Decomposition coefficients within +- this rate window will be combined
min_correlation_distance_to_averagine
Minimum difference in correlation between incorporation pattern and averagine pattern. Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values <= -1
pattern_15N_TIC_threshold
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_13C_TIC_threshold
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_2H_TIC_threshold
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_18O_TIC_threshold
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
heatmap_bins
Number of RIA bins for heat map generation.
plot_extension
Extension used for plots (png|svg|pdf).
qc_output_directory
Output directory for the quality report
labeling_element
Which element (single letter code) is labeled.
use_unassigned_ids
Include identifications not assigned to a feature in pattern detection.
use_averagine_ids
Use averagine peptides as model to perform pattern detection on unidentified peptides.
report_natural_peptides
Whether purely natural peptides are reported in the quality report.
filter_monoisotopic
Try to filter out mono-isotopic patterns to improve detection of low RIA patterns
cluster
Perform grouping
observed_peak_fraction
Fraction of observed/expected peaks.
min_consecutive_isotopes
Minimum number of consecutive isotopic intensities needed.
score_plot_yaxis_min
The minimum value of the score axis. Values smaller than zero usually only make sense if the observed peak fraction is set to 0.
collect_method
How RIAs are collected.
lowRIA_correlation_threshold
Correlation threshold for reporting low RIA patterns. Disable and take correlation_threshold value for negative values.
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)

Input Ports

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Centroided MS1 data [mzML]
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Protein sequence database [fasta]
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Feature data annotated with identifications (IDMapper) [featureXML]
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Path to the R executable (default: 'R') [,opt.]

Output Ports

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Column separated file with feature fitting result. [csv]
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Column separated file with peptide centric result. [csv]

Views

MetaProSIP Std Output
The text sent to standard out during the execution of MetaProSIP.
MetaProSIP Error Output
The text sent to standard error during the execution of MetaProSIP. (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)

Installation

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

KNIME 4.2
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Developers

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