OpenSwathRTNormalizer

Options

version

Version of the tool that generated this parameters file.

min_rsq

Minimum r-squared of RT peptides regression

min_coverage

Minimum relative amount of RT peptides to keep

estimateBestPeptides

Whether the algorithms should try to choose the best peptides based on their peak shape for normalization. Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides).

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)

outlierMethod

Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none'). Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides).

useIterativeChauvenet

Whether to use Chauvenet's criterion when using iterative methods. This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained.

RANSACMaxIterations

Maximum iterations for the RANSAC outlier detection algorithm.

RANSACMaxPercentRTThreshold

Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient). Default is set to 3% which is around +/- 4 minutes on a 120 gradient.

RANSACSamplingSize

Sampling size of data points per iteration for the RANSAC outlier detection algorithm.

stop_report_after_feature

Stop reporting after feature (ordered by quality; -1 means do not stop).

rt_extraction_window

Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution). For this to work, the TraML input file needs to contain normalized RT values.

rt_normalization_factor

The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)

quantification_cutoff

Cutoff in m/z below which peaks should not be used for quantification any more

write_convex_hull

Whether to write out all points of all features into the featureXML

spectrum_addition_method

For spectrum addition, either use simple concatenation or use peak resampling

add_up_spectra

Add up spectra around the peak apex (needs to be a non-even integer)

spacing_for_spectra_resampling

If spectra are to be added, use this spacing to add them up

uis_threshold_sn

S/N threshold to consider identification transition (set to -1 to consider all)

uis_threshold_peak_area

Peak area threshold to consider identification transition (set to -1 to consider all)

scoring_model

Scoring model to use

im_extra_drift

Extra drift time to extract for IM scoring (as a fraction, e.g. 0.25 means 25% extra on each side)

strict

Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram.

use_ms1_ion_mobility

Performs ion mobility extraction in MS1. Set to false if MS1 spectra do not contain ion mobility

stop_after_feature

Stop finding after feature (ordered by intensity; -1 means do not stop).

stop_after_intensity_ratio

Stop after reaching intensity ratio

min_peak_width

Minimal peak width (s), discard all peaks below this value (-1 means no action).

peak_integration

Calculate the peak area and height either the smoothed or the raw chromatogram data.

background_subtraction

Remove background from peak signal using estimated noise levels. The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation.

recalculate_peaks

Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if the variation within the picked peaks is too large.

use_precursors

Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)

use_consensus

Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)

recalculate_peaks_max_z

Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).

minimal_quality

Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold

resample_boundary

For computing peak quality, how many extra seconds should be sample left and right of the actual peak

compute_peak_quality

Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.

compute_peak_shape_metrics

Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.

compute_total_mi

Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.

boundary_selection_method

Method to use when selecting the best boundaries for peaks.

sgolay_frame_length

The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.

sgolay_polynomial_order

Order of the polynomial that is fitted.

gauss_width

Gaussian width in seconds, estimated peak size.

use_gauss

Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)

peak_width

Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.

signal_to_noise

Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.

sn_win_len

Signal to noise window length.

sn_bin_count

Signal to noise bin count.

write_sn_log_messages

Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin

remove_overlapping_peaks

Try to remove overlapping peaks during peak picking

method

Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).

integration_type

The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration.

baseline_type

The baseline type to use in estimateBackground() based on the peak boundaries. A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base).

fit_EMG

Fit the chromatogram/spectrum to the EMG peak model.

dia_extraction_window

DIA extraction window in Th or ppm.

dia_extraction_unit

DIA extraction window unit

dia_centroided

Use centroided DIA data.

dia_byseries_intensity_min

DIA b/y series minimum intensity to consider.

dia_byseries_ppm_diff

DIA b/y series minimal difference in ppm to consider.

dia_nr_isotopes

DIA number of isotopes to consider.

dia_nr_charges

DIA number of charges to consider.

peak_before_mono_max_ppm_diff

DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic.

interpolation_step

Sampling rate for the interpolation of the model function.

tolerance_stdev_bounding_box

Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.

max_iteration

Maximum number of iterations using by Levenberg-Marquardt algorithm.

init_mom

Initialize parameters using method of moments estimators.

mean

Centroid position of the model.

variance

Variance of the model.

use_shape_score

Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)

use_coelution_score

Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)

use_rt_score

Use the retention time score (this score measure the difference in retention time)

use_library_score

Use the library score

use_elution_model_score

Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)

use_intensity_score

Use the intensity score

use_nr_peaks_score

Use the number of peaks score

use_total_xic_score

Use the total XIC score

use_total_mi_score

Use the total MI score

use_sn_score

Use the SN (signal to noise) score

use_mi_score

Use the MI (mutual information) score

use_dia_scores

Use the DIA (SWATH) scores. If turned off, will not use fragment ion spectra for scoring.

use_ms1_correlation

Use the correlation scores with the MS1 elution profiles

use_sonar_scores

Use the scores for SONAR scans (scanning swath)

use_ion_mobility_scores

Use the scores for Ion Mobility scans

use_ms1_fullscan

Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)

use_ms1_mi

Use the MS1 MI score

use_uis_scores

Use UIS scores for peptidoform identification

use_peak_shape_metrics

Use peak shape metrics for scoring

use_ionseries_scores

Use MS2-level b/y ion-series scores for peptidoform identification

use_ms2_isotope_scores

Use MS2-level isotope scores (pearson & manhattan) across product transitions (based on ID if annotated or averagine)

InitialQualityCutoff

The initial overall quality cutoff for a peak to be scored (range ca. -2 to 2)

OverallQualityCutoff

The overall quality cutoff for a peak to go into the retention time estimation (range ca. 0 to 10)

NrRTBins

Number of RT bins to use to compute coverage. This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)

MinPeptidesPerBin

Minimal number of peptides that are required for a bin to counted as 'covered'

MinBinsFilled

Minimal number of bins required to be covered

Views

OpenSwathRTNormalizer Std Output

The text sent to standard out during the execution of OpenSwathRTNormalizer.

OpenSwathRTNormalizer Error Output

The text sent to standard error during the execution of OpenSwathRTNormalizer. (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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