MetaProSIP

Options

version

Version of the tool that generated this parameters file.

mz_tolerance_ppm

Tolerance in ppm

rt_tolerance_s

Tolerance 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)

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.)

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