| OpenMS 2.5.0

OpenSwathWorkflow

Complete workflow to run OpenSWATH

This implements the OpenSWATH workflow as described in Rost and Rosenberger et al. (Nature Biotechnology, 2014) and provides a complete, integrated analysis tool without the need to run multiple tools consecutively. See also http://openswath.org/ for additional documentation.

It executes the following steps in order, which is implemented in OpenSwathWorkflow:

- Reading of input files, which can be provided as one single mzML or multiple "split" mzMLs (one per SWATH)
- Computing the retention time transformation using RT-normalization peptides
- Reading of the transition list
- Extracting the specified transitions
- Scoring the peak groups in the extracted ion chromatograms (XIC)
- Reporting the peak groups and the chromatograms

See below or have a look at the INI file (via "OpenSwathWorkflow -write_ini myini.ini") for available parameters and more functionality.

### Input: SWATH maps and assay library (transition list)

SWATH maps can be provided as mzML files, either as single file directly from the machine (this assumes that the SWATH method has 1 MS1 and then n MS2 spectra which are ordered the same way for each cycle). E.g. a valid method would be MS1, MS2 [400-425], MS2 [425-450], MS1, MS2 [400-425], MS2 [425-450] while an invalid method would be MS1, MS2 [400-425], MS2 [425-450], MS1, MS2 [425-450], MS2 [400-425] where MS2 [xx-yy] indicates an MS2 scan with an isolation window starting at xx and ending at yy. OpenSwathWorkflow will try to read the SWATH windows from the data, if this is not possible please provide a tab-separated list with the correct windows using the -swath_windows_file parameter (this is recommended). Note that the software expects extraction windows (e.g. which peptides to extract from which window) which cannot have overlaps, otherwise peptides will be extracted from two different windows.

Alternatively, a set of split files (n+1 mzML files) can be provided, each containing one SWATH map (or MS1 map).

Since the file size can become rather large, it is recommended to not load the whole file into memory but rather cache it somewhere on the disk using a fast-access data format. This can be specified using the -readOptions cache parameter (this is recommended!).

The assay library (transition list) is provided through the `-tr` parameter and can be in one of the following formats:

- TraML
- OpenSWATH TSV transition lists
- OpenSWATH PQP SQLite files
- SpectraST MRM transition lists
- Skyline transition lists
- Spectronaut transition lists

### Parameters

The current parameters are optimized for 2 hour gradients on SCIEX 5600 / 6600 TripleTOF instruments with a peak width of around 30 seconds using iRT peptides. If your chromatography differs, please consider adjusting `-Scoring`:TransitionGroupPicker:min_peak_width to allow for smaller or larger peaks and adjust the `-rt_extraction_window` to use a different extraction window for the retention time. In m/z domain, consider adjusting `-mz_extraction_window` to your instrument resolution, which can be in Th or ppm.

Furthermore, if you wish to use MS1 information, use the `-use_ms1_traces` flag and provide an MS1 map in addition to the SWATH data.

If you encounter issues with peak picking, try to disable peak filtering by setting `-Scoring`:TransitionGroupPicker:compute_peak_quality false which will disable the filtering of peaks by chromatographic quality. Furthermore, you can adjust the smoothing parameters for the peak picking, by adjusting `-Scoring`:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length or using a Gaussian smoothing based on your estimated peak width. Adjusting the signal to noise threshold will make the peaks wider or smaller.

### Output: Feature list and chromatograms

The output of the OpenSwathWorkflow is a feature list, either as FeatureXML or as tsv (use `-out_features` or `-out_tsv`) while the latter is more memory friendly and can be directly used as input to other tools such as mProphet or pyProphet. If you analyze large datasets, it is recommended to only use `-out_tsv` and not `-out_features`. For downstream analysis (e.g. using mProphet or pyProphet) also the `-out_tsv` format is recommended.

The feature list generated by `-out_tsv` is a tab-separated file. It can be used directly as input to the mProphet or pyProphet (a Python re-implementation of mProphet) software tool, see Reiter et al (2011, Nature Methods).

In addition, the extracted chromatograms can be written out using the `-out_chrom` parameter.

#### Feature list output format

The tab-separated feature output contains the following information:

Header row | Format | Description
transition_group_id | String | A unique id for the transition group (all chromatographic traces that are analyzed together)
peptide_group_label | String | A unique id for the peptide group (will be the same for each charge state and heavy/light status)
run_id | String | An identifier for the run (currently always 0)
filename | String | The input filename
RT | Float | Peak group retention time
id | String | A unique identifier for the peak group
Sequence | String | Peptide sequence (no modifications)
MC | Int | Missed cleavages of the sequence (assuming Trypsin as protease)
FullPeptideName | String | Full peptide sequence including modifications in Unimod format
Charge | Int | Assumed charge state
m/z | Float | Precursor m/z
masserror_ppm | Float List | Pairs of fragment masses (m/z) and their associated error in ppm for all transitions
Intensity | Float | Peak group intensity (sum of all transitions)
ProteinName | String | Name of the associated protein
decoy | String | Whether the transition is decoy or not (0 = false, 1 = true)
assay_rt | Float | The expected RT in seconds (based on normalized iRT value)
delta_rt | Float | The difference between the expected RT and the peak group RT in seconds
leftWidth | Float | The start of the peak group (left side) in seconds
main_var_xx_swath_prelim_score | Float | Initial score
norm_RT | Float | The peak group retention time in normalized (iRT) space
nr_peaks | Int | The number of transitions used
peak_apices_sum | Float | The sum of all peak apices (may be used as alternative intensity)
potentialOutlier | String | Potential outlier transitions (or "none" if none was detected)
rightWidth | Float | The end of the peak group (left side) in seconds
rt_score | Float | The raw RT score (unnormalized)
sn_ratio | Float | The raw S/N ratio
total_xic | Float | The total XIC of the chromatogram
var_... | Float | One of multiple sub-scores used by OpenSWATH to describe the peak group
aggr_prec_Peak_Area | String | Intensity (peak area) of MS1 traces separated by semicolon
aggr_prec_Peak_Apex | String | Intensity (peak apex) of MS1 traces separated by semicolon
aggr_prec_Fragment_Annotation | String | Annotation of MS1 traces separated by semicolon
aggr_Peak_Area | String | Intensity (peak area) of fragment ion traces separated by semicolon
aggr_Peak_Apex | String | Intensity (peak apex) of fragment ion traces separated by semicolon
aggr_Fragment_Annotation | String | Annotation of fragment ion traces separated by semicolon

### Execution flow:

The overall execution flow for this tool is implemented in OpenSwathWorkflow.

The command line parameters of this tool are:

    OpenSwathWorkflow -- Complete workflow to run OpenSWATH

    Full documentation: http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      OpenSwathWorkflow <options>

    This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript

    ion or use the --helphelp option.

    Options (mandatory options marked with '*'):

      -in <files>*                        Input files separated by blank (valid formats: 'mzML', 'mzXML', 'sqMass

                                          ')

      -tr <file>*                         Transition file ('TraML','tsv','pqp') (valid formats: 'traML', 'tsv',

                                          'pqp')

      -tr_type <type>                     Input file type -- default: determined from file extension or content

                                          (valid: 'traML', 'tsv', 'pqp')

      -tr_irt <file>                      Transition file ('TraML') (valid formats: 'traML', 'tsv', 'pqp')

      -tr_irt_nonlinear <file>            Additional nonlinear transition file ('TraML') (valid formats: 'traML',

                                          'tsv', 'pqp')

      -out_features <file>                Output file (valid formats: 'featureXML')

      -out_tsv <file>                     TSV output file (mProphet-compatible TSV file) (valid formats: 'tsv')

      -out_osw <file>                     OSW output file (PyProphet-compatible SQLite file) (valid formats: 'osw

                                          ')

      -sonar                              Data is scanning SWATH data

      -rt_extraction_window <double>      Only extract RT around this value (-1 means extract over the whole rang

                                          e, a value of 600 means to extract around +/- 300 s of the expected

                                          elution). (default: '600.0')

      -ion_mobility_window <double>       Extraction window in ion mobility dimension (in milliseconds). This is

                                          the full window size, e.g. a value of 10 milliseconds would extract 5

                                          milliseconds on either side. (default: '-1.0')

      -mz_extraction_window <double>      Extraction window in Thomson or ppm (see mz_extraction_window_unit)

                                          (default: '0.05' min: '0.0')

      -mz_extraction_window_ms1 <double>  Extraction window used in MS1 in Thomson or ppm (see mz_extraction_wind

                                          ow_ms1_unit) (default: '0.05' min: '0.0')

      -im_extraction_window_ms1 <double>  Extraction window in ion mobility dimension for MS1 (in milliseconds).

                                          (default: '-1.0')

    Debugging:

      -Debugging:irt_mzml <file>          Chromatogram mzML containing the iRT peptides (valid formats: 'mzML')

      -Debugging:irt_trafo <file>         Transformation file for RT transform (valid formats: 'trafoXML')

    Common UTIL 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)

    The following configuration subsections are valid:

     - Calibration       Parameters for the m/z and ion mobility calibration.

     - Library           Library parameters section

     - RTNormalization   Parameters for the RTNormalization for iRT petides. This specifies how the RT alignment

                         is performed and how outlier detection is applied. Outlier detection can be done iterati

                         vely (by default) which removes one outlier per iteration or using the RANSAC algorithm.

     - Scoring           Scoring parameters section

    You can write an example INI file using the '-write_ini' option.

    Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+OpenSwathWorkflow Complete workflow to run OpenSWATH
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'OpenSwathWorkflow'
in[] Input files separated by blank input file*.mzML,*.mzXML,*.sqMass
tr transition file ('TraML','tsv','pqp')input file*.traML,*.tsv,*.pqp
tr_type input file type -- default: determined from file extension or content
traML,tsv,pqp
tr_irt transition file ('TraML')input file*.traML,*.tsv,*.pqp
tr_irt_nonlinear additional nonlinear transition file ('TraML')input file*.traML,*.tsv,*.pqp
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.input file*.trafoXML
swath_windows_file Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset. Note that the first line is a header and will be skipped.input file
sort_swath_maps false Sort input SWATH files when matching to SWATH windows from swath_windows_file true,false
use_ms1_traces false Extract the precursor ion trace(s) and use for scoring true,false
enable_uis_scoring false Enable additional scoring of identification assays true,false
out_features output file output file*.featureXML
out_tsv TSV output file (mProphet-compatible TSV file)output file*.tsv
out_osw OSW output file (PyProphet-compatible SQLite file)output file*.osw
out_chrom Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format)output file*.mzML,*.sqMass
out_qc Optional QC meta data (charge distribution in MS1). Only works with mzML input files.output file*.json
min_upper_edge_dist 0.0 Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson
sonar false data is scanning SWATH data true,false
rt_extraction_window 600.0 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 0.0 Output an XIC with a RT-window by this much larger (e.g. to visually inspect a larger area of the chromatogram)0.0:∞
ion_mobility_window-1.0 Extraction window in ion mobility dimension (in milliseconds). This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side.
mz_extraction_window 0.05 Extraction window in Thomson or ppm (see mz_extraction_window_unit)0.0:∞
mz_extraction_window_unit Th Unit for mz extraction Th,ppm
mz_extraction_window_ms1 0.05 Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)0.0:∞
mz_extraction_window_ms1_unit Th Unit of the MS1 m/z extraction window ppm,Th
im_extraction_window_ms1-1.0 Extraction window in ion mobility dimension for MS1 (in milliseconds).
use_ms1_ion_mobility true Also perform precursor extraction using the same ion mobility window as for fragment ion extraction true,false
matching_window_only false 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).true,false
irt_mz_extraction_window 0.05 Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)0.0:∞
irt_mz_extraction_window_unit Th Unit for mz extraction Th,ppm
irt_im_extraction_window-1.0 Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)
min_rsq 0.95 Minimum r-squared of RT peptides regression
min_coverage 0.6 Minimum relative amount of RT peptides to keep
split_file_input false The input files each contain one single SWATH (alternatively: all SWATH are in separate files)true,false
use_elution_model_score false Turn on elution model score (EMG fit to peak)true,false
readOptions normal 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 normal,cache,cacheWorkingInMemory,workingInMemory
mz_correction_function none Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra.none,regression_delta_ppm,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm
tempDirectory C:/Users/ppant/AppData/Local/Temp Temporary directory to store cached files for example
extraction_function tophat Function used to extract the signal tophat,bartlett
batchSize 250 The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)0:∞
outer_loop_threads-1 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 0 The number of MS1 isotopes used for extraction 0:∞
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++Debugging Debugging
irt_mzml Chromatogram mzML containing the iRT peptides output file*.mzML
irt_trafo Transformation file for RT transform output file*.trafoXML
+++Calibration Parameters for the m/z and ion mobility calibration.
ms1_im_calibration false Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)true,false
im_correction_function linear Type of normalization function for IM calibration.none,linear
debug_im_file Debug file for Ion Mobility calibration.
debug_mz_file Debug file for m/z calibration.
+++Library Library parameters section
retentionTimeInterpretation iRT How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)iRT,seconds,minutes
override_group_label_check false 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.true,false
force_invalid_mods false Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)true,false
+++RTNormalization Parameters for the RTNormalization for iRT petides. This specifies how the RT alignment is performed and how outlier detection is applied. Outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm.
alignmentMethod linear 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.linear,interpolated,lowess,b_spline
outlierMethod iter_residual 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).iter_residual,iter_jackknife,ransac,none
useIterativeChauvenet false 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.true,false
RANSACMaxIterations 1000 Maximum iterations for the RANSAC outlier detection algorithm.
RANSACMaxPercentRTThreshold 3 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 10 Sampling size of data points per iteration for the RANSAC outlier detection algorithm.
estimateBestPeptides false 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).true,false
InitialQualityCutoff 0.5 The initial overall quality cutoff for a peak to be scored (range ca. -2 to 2)
OverallQualityCutoff 5.5 The overall quality cutoff for a peak to go into the retention time estimation (range ca. 0 to 10)
NrRTBins 10 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 1 Minimal number of peptides that are required for a bin to counted as 'covered'
MinBinsFilled 8 Minimal number of bins required to be covered
++++lowess
span 0.666666666666667 Span parameter for lowess 0.0:1.0
++++b_spline
num_nodes 5 Number of nodes for b spline 0:∞
+++Scoring Scoring parameters section
stop_report_after_feature 5 Stop reporting after feature (ordered by quality; -1 means do not stop).
rt_normalization_factor 100.0 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 0.0 Cutoff in m/z below which peaks should not be used for quantification any more 0.0:∞
write_convex_hull false Whether to write out all points of all features into the featureXML true,false
spectrum_addition_method simple For spectrum addition, either use simple concatenation or use peak resampling simple,resample
add_up_spectra 1 Add up spectra around the peak apex (needs to be a non-even integer)1:∞
spacing_for_spectra_resampling 0.005 If spectra are to be added, use this spacing to add them up 0.0:∞
uis_threshold_sn 0 S/N threshold to consider identification transition (set to -1 to consider all)
uis_threshold_peak_area 0 Peak area threshold to consider identification transition (set to -1 to consider all)
scoring_model default Scoring model to use default,single_transition
im_extra_drift 0.0 Extra drift time to extract for IM scoring (as a fraction, e.g. 0.25 means 25% extra on each side)0.0:∞
++++TransitionGroupPicker
stop_after_feature-1 Stop finding after feature (ordered by intensity; -1 means do not stop).
min_peak_width-1.0 Minimal peak width (s), discard all peaks below this value (-1 means no action).
peak_integration original Calculate the peak area and height either the smoothed or the raw chromatogram data.original,smoothed
background_subtraction none 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.none,original,exact
recalculate_peaks true 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.true,false
use_precursors false Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)true,false
use_consensus true Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)true,false
recalculate_peaks_max_z 0.75 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-1.5 Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
resample_boundary 15.0 For computing peak quality, how many extra seconds should be sample left and right of the actual peak
compute_peak_quality true 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.true,false
compute_peak_shape_metrics false Calculates various peak shape metrics (e.g., tailing) that can be used for downstream QC/QA.true,false
compute_total_mi false Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring.true,false
boundary_selection_method largest Method to use when selecting the best boundaries for peaks.largest,widest
+++++PeakPickerMRM
sgolay_frame_length 11 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 3 Order of the polynomial that is fitted.
gauss_width 30.0 Gaussian width in seconds, estimated peak size.
use_gauss false Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)false,true
peak_width-1.0 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 0.1 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.0.0:∞
write_sn_log_messages false Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin true,false
remove_overlapping_peaks true Try to remove overlapping peaks during peak picking false,true
method corrected Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).legacy,corrected,crawdad
+++++PeakIntegrator
integration_type intensity_sum The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration.intensity_sum,simpson,trapezoid
baseline_type base_to_base 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).base_to_base,vertical_division,vertical_division_min,vertical_division_max
fit_EMG false Fit the chromatogram/spectrum to the EMG peak model.false,true
++++DIAScoring
dia_extraction_window 0.05 DIA extraction window in Th or ppm.0.0:∞
dia_extraction_unit Th DIA extraction window unit Th,ppm
dia_centroided false Use centroided DIA data.true,false
dia_byseries_intensity_min 300.0 DIA b/y series minimum intensity to consider.0.0:∞
dia_byseries_ppm_diff 10.0 DIA b/y series minimal difference in ppm to consider.0.0:∞
dia_nr_isotopes 4 DIA number of isotopes to consider.0:∞
dia_nr_charges 4 DIA number of charges to consider.0:∞
peak_before_mono_max_ppm_diff 20.0 DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic.0.0:∞
++++EMGScoring
max_iteration 10 Maximum number of iterations using by Levenberg-Marquardt algorithm.
++++Scores
use_shape_score true Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)true,false
use_coelution_score true Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)true,false
use_rt_score true Use the retention time score (this score measure the difference in retention time)true,false
use_library_score true Use the library score true,false
use_intensity_score true Use the intensity score true,false
use_nr_peaks_score true Use the number of peaks score true,false
use_total_xic_score true Use the total XIC score true,false
use_total_mi_score false Use the total MI score true,false
use_sn_score true Use the SN (signal to noise) score true,false
use_mi_score false Use the MI (mutual information) score true,false
use_dia_scores true Use the DIA (SWATH) scores. If turned off, will not use fragment ion spectra for scoring.true,false
use_ms1_correlation false Use the correlation scores with the MS1 elution profiles true,false
use_sonar_scores false Use the scores for SONAR scans (scanning swath)true,false
use_ion_mobility_scores false Use the scores for Ion Mobility scans true,false
use_ms1_fullscan false Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)true,false
use_ms1_mi false Use the MS1 MI score true,false
use_uis_scores false Use UIS scores for peptidoform identification true,false