OpenSwathWorkflow

Options

version

Version of the tool that generated this parameters file.

tr_type

input file type -- default: determined from file extension or content

auto_irt

Whether to sample iRTs on‐the‐fly (true) from the input targeted transition file (instead of passing specific iRT files). This may be useful if standard iRTs (Biognosys iRT kit) were not spiked-in. If set to false, and no additional iRT files are provided via `-tr_irt` / `-tr_irt_nonlinear`, and no transformation is provided via `-rt_norm`, then no calibration is performed.

sort_swath_maps

Sort input SWATH files when matching to SWATH windows from swath_windows_file

enable_ms1

Extract the precursor ion trace(s) and use for scoring if present

enable_ipf

Enable additional scoring of identification assays using IPF (see online documentation)

out_features_type

input file type -- default: determined from file extension or content

min_upper_edge_dist

Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson

pasef

data is PASEF data

estimate_extraction_windows

Choose which extraction windows to estimate during iRT calibration. 'all' = estimate RT, m/z, and IM windows; 'none' = use user-set windows; or a comma-separated list from {rt,mz,im}.

rt_estimation_padding_factor

A padding factor to multiply the estimated RT window by. For example, a factor of 1.3 will add a 30% padding to the estimated RT window, so if the estimated RT window is 144, then 43 will be added for a total estimated RT window of 187 seconds. A factor of 1.0 will not add any padding to the estimated window.

im_estimation_padding_factor

A padding factor to multiply the estimated ion_mobility window by. For example, a factor of 1.3 will add a 30% padding to the estimated ion_mobility window, so if the estimated ion_mobility window is 0.03, then 0.009 will be added for a total estimated ion_mobility window of 0.039. A factor of 1.0 will not add any padding to the estimated window.

mz_estimation_padding_factor

A padding factor to multiply the estimated m/z window by. For example, a factor of 1.3 will add a 30% padding to the estimated m/z window, so if the estimated m/z window is 18, then 5.4 will be added for a total estimated m/z window of 23.4. A factor of 1.0 will not add any padding to the estimated window.

rt_extraction_window

Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution).

extra_rt_extraction_window

Output an XIC with a RT-window by this much larger (e.g. to visually inspect a larger area of the chromatogram)

ion_mobility_window

Extraction window in ion mobility dimension (in 1/k0 or milliseconds depending on library). This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side. -1 means extract over the whole range or ion mobility is not present. (Default for diaPASEF data: 0.06 1/k0)

mz_extraction_window

Extraction window in Thomson or ppm (see mz_extraction_window_unit)

mz_extraction_window_unit

Unit for mz extraction

mz_extraction_window_ms1

Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)

mz_extraction_window_ms1_unit

Unit of the MS1 m/z extraction window

im_extraction_window_ms1

Extraction window in ion mobility dimension for MS1 (in 1/k0 or milliseconds depending on library). -1 means this is not ion mobility data.

use_ms1_ion_mobility

Also perform precursor extraction using the same ion mobility window as for fragment ion extraction

matching_window_only

Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows. Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows).

irt_mz_extraction_window

Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)

irt_mz_extraction_window_unit

Unit for mz extraction

irt_im_extraction_window

Ion mobility extraction window used for iRT (in 1/K0 or milliseconds depending on library). -1 means do not perform ion mobility calibration

irt_nonlinear_rt_extraction_window

Only extract RT around this value for non linear iRT calibration (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution).

min_rsq

Minimum r-squared of RT peptides regression

min_coverage

Minimum relative amount of RT peptides to keep

split_file_input

The input files each contain one single SWATH (alternatively: all SWATH are in separate files)

use_elution_model_score

Turn on elution model score (EMG fit to peak)

readOptions

Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first. If you choose cache, make sure to also set tempDirectory

mz_correction_function

Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra.

tempDirectory

Temporary directory to store cached files for example

extraction_function

Function used to extract the signal

batchSize

The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)

outer_loop_threads

How many threads should be used for the outer loop (-1 use all threads, use 4 to analyze 4 SWATH windows in memory at once).

ms1_isotopes

The number of MS1 isotopes used for extraction

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)

irt_bins

Number of RT bins for sampling. (When `auto_irt` is set to 'true')

irt_peptides_per_bin

Peptides sampled per bin. (When `auto_irt` is set to 'true')

irt_seed

RNG seed (0 = non‐deterministic). (When `auto_irt` is set to 'true')

irt_bins_nonlinear

Number of RT bins for sampling. (When `auto_irt` is set to 'true')

irt_peptides_per_bin_nonlinear

Peptides sampled per bin for additional nonlinear calibration. If 0, nonlinear calibration will not be performed. (When `auto_irt` is set to 'true')

tr_irt

transition file ('TraML') for linear iRTs. Takes precedent even when `auto_rt` is set to 'true'

tr_irt_nonlinear

additional nonlinear transition file ('TraML'). Takes precedent even when `auto_rt` is set to 'true'

tr_irt_priority_sampling

Optional custom transition file (TSV format only) containing additional priority peptides for iRT sampling. These peptides will be prioritized alongside the built-in irtkit and cirtkit peptides when `auto_irt` is enabled. Useful for including project-specific or custom iRT peptides.

rt_norm

RT normalization file (how to map the RTs of this run to the ones stored in the library). If set, tr_irt may be omitted.

mz_extraction_window

M/z extraction window width

mz_extraction_window_ppm

Whether m/z extraction is in ppm

ms1_im_calibration

Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)

im_extraction_window

Ion mobility extraction window width

mz_estimation_padding_factor

A padding factor to multiply the estimated m/z window by. For example, a factor of 1.3 will add a 30% padding to the estimated m/z window, so if the estimated m/z window is 18, then 5.4 will be added for a total estimated m/z window of 23.4. A factor of 1.0 will not add any padding to the estimated window.

im_estimation_padding_factor

A padding factor to multiply the estimated ion_mobility window by. For example, a factor of 1.3 will add a 30% padding to the estimated ion_mobility window, so if the estimated ion_mobility window is 0.03, then 0.009 will be added for a total estimated ion_mobility window of 0.039. A factor of 1.0 will not add any padding to the estimated window.

mz_correction_function

Type of normalization function for m/z calibration.

im_correction_function

Type of normalization function for IM calibration.

debug_im_file

Debug file for Ion Mobility calibration.

debug_mz_file

Debug file for m/z calibration.

alignmentMethod

How to perform the alignment to the normalized RT space using anchor points. 'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing.

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.

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).

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

auto_span

If true, or if 'span' is 0, automatically select LOWESS span by cross-validation.

span

Span parameter for lowess

auto_span_min

Lower bound for auto-selected span.

auto_span_max

Upper bound for auto-selected span.

auto_span_grid

Optional explicit grid of span candidates in (0,1]. Comma-separated list, e.g. '0.2,0.3,0.5'. If empty, a default grid is used.

num_nodes

Number of nodes for b spline

retentionTimeInterpretation

How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)

override_group_label_check

Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group). Only turn this off if you know what you are doing.

force_invalid_mods

Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)

stop_report_after_feature

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

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

spectrum_merge_method_type

For spectrum addition, either use a fixed number of spectra or dynamically select the number of spectra to add around the peak apex based on the merge_spectra_by_peak_width_fraction.

add_up_spectra

Add up spectra on the left and right around the retention time peak apex.

spacing_for_spectra_resampling

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

merge_spectra_by_peak_width_fraction

If spectra are to be added based on the peak width of peak, construct number of spectra to be added based on N percent of number of points of peak width.

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

apply_im_peak_picking

Perform peak picking on the extracted ion mobilograms. This is useful for reducing intefering signals from co-eluting analytes in the ion mobility dimension. The peak picking will take the highest peak and discard the remaining peaks for ion mobility scoring.

stop_after_feature

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

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.

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.

max_iteration

Maximum number of iterations using by Levenberg-Marquardt algorithm.

init_mom

Initialize parameters using method of moments estimators.

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_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_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)

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