MetaProSIP

Performs proteinSIP on peptide features for elemental flux analysis.

The command line parameters of this tool are:

MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis.
Full documentation: http://www.openms.de/doxygen/release/3.1.0/html/TOPP_MetaProSIP.html
Version: 3.1.0 Oct 18 2023, 10:27:18, Revision: 17a07f8
To cite OpenMS:
 + Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for 
   mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  MetaProSIP <options>

Options (mandatory options marked with '*'):
  -in_mzML <file>*                  Centroided MS1 data (valid formats: 'mzML')
  -in_fasta <file>*                 Protein sequence database (valid formats: 'fasta')
  -out_csv <file>*                  Column separated file with feature fitting result. (valid formats: 'csv')

  -out_peptide_centric_csv <file>*  Column separated file with peptide centric result. (valid formats: 'csv')

  -in_featureXML <file>*            Feature data annotated with identifications (IDMapper) (valid formats: 
                                    'featureXML')
  -r_executable <file>              Path to the R executable (default: 'R')
  -mz_tolerance_ppm <tol>           Tolerance in ppm (default: '10.0')
  -rt_tolerance_s <tol>             Tolerance window around feature rt for XIC extraction (default: '30.0')
  -intensity_threshold <tol>        Intensity threshold to collect peaks in the MS1 spectrum. (default: '10.0
                                    ')
  -correlation_threshold <tol>      Correlation threshold for reporting a RIA (default: '0.7')
  -xic_threshold <tol>              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. (default:
                                     '0.7')
  -decomposition_threshold <tol>    Minimum R-squared of decomposition that must be achieved for a peptide 
                                    to be reported. (default: '0.7')
  -weight_merge_window <tol>        Decomposition coefficients within +- this rate window will be combined 
                                    (default: '5.0')
  -plot_extension <extension>       Extension used for plots (png|svg|pdf). (default: 'png') (valid: 'png', 
                                    'svg', 'pdf')
  -qc_output_directory <directory>  Output directory for the quality report
  -labeling_element <parameter>     Which element (single letter code) is labeled. (default: 'C') (valid: 
                                    'C', 'N', 'H', 'O')
  -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 unidentif
                                    ied 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
                                    
Common TOPP options:
  -ini <file>                       Use the given TOPP INI file
  -threads <n>                      Sets the number of threads allowed to be used by the TOPP tool (default: 
                                    '1')
  -write_ini <file>                 Writes the default configuration file
  --help                            Shows options
  --helphelp                        Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MetaProSIPPerforms proteinSIP on peptide features for elemental flux analysis.

version3.1.0 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 Path to the R executable (default: 'R')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