Performs proteinSIP on peptide features for elemental flux analysis.
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required parameter
advanced parameter
+MetaProSIPPerforms proteinSIP on peptide features for elemental flux analysis.
version3.3.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'MetaProSIP'
in_mzML
Centroided MS1 datainput file*.mzML
in_fasta
Protein sequence databaseinput file*.fasta
out_csv
Column separated file with feature fitting result.output file*.csv
out_peptide_centric_csv
Column separated file with peptide centric result.output file*.csv
in_featureXML
Feature data annotated with identifications (IDMapper)input file*.featureXML
r_executableR
The R executable. Provide a full or relative path, or make sure it can be found in your PATH environment.input file, is_executable
mz_tolerance_ppm10.0
Tolerance in ppm
rt_tolerance_s30.0
Tolerance window around feature rt for XIC extraction
intensity_threshold10.0
Intensity threshold to collect peaks in the MS1 spectrum.
correlation_threshold0.7
Correlation threshold for reporting a RIA
xic_threshold0.7
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_threshold0.7
Minimum R-squared of decomposition that must be achieved for a peptide to be reported.
weight_merge_window5.0
Decomposition coefficients within +- this rate window will be combined
min_correlation_distance_to_averagine-1.0
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_threshold0.95
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_13C_TIC_threshold0.95
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_2H_TIC_threshold0.95
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
pattern_18O_TIC_threshold0.95
The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account.
heatmap_bins20
Number of RIA bins for heat map generation.
plot_extensionpng
Extension used for plots (png|svg|pdf).png, svg, pdf
qc_output_directory
Output directory for the quality report
labeling_elementC
Which element (single letter code) is labeled.C, N, H, O
use_unassigned_idsfalse
Include identifications not assigned to a feature in pattern detection.true, false
use_averagine_idsfalse
Use averagine peptides as model to perform pattern detection on unidentified peptides.true, false
report_natural_peptidesfalse
Whether purely natural peptides are reported in the quality report.true, false
filter_monoisotopicfalse
Try to filter out mono-isotopic patterns to improve detection of low RIA patternstrue, false
clusterfalse
Perform groupingtrue, false
observed_peak_fraction0.5
Fraction of observed/expected peaks.
min_consecutive_isotopes2
Minimum number of consecutive isotopic intensities needed.
score_plot_yaxis_min0.0
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_methodcorrelation_maximum
How RIAs are collected.correlation_maximum, decomposition_maximum
lowRIA_correlation_threshold-1.0
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)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue, false
forcefalse
Overrides tool-specific checkstrue, false
testfalse
Enables the test mode (needed for internal use only)true, false