FLASHDeconv

FLASHDeconv performs ultrafast deconvolution of top down proteomics MS datasets. FLASHDeconv takes mzML file as input and outputs deconvolved feature list (.tsv) and deconvolved spectra files (.tsv, .mzML, .msalign, .ms1ft). FLASHDeconv uses SpectralDeconvolution for spectral level deconvolution and MassFeatureTracer to detect mass features. Also for MSn spectra, the precursor masses (not peak m/zs) should be determined and assigned in most cases. This assignment can be done by tracking MSn-1 spectra deconvolution information. Thus FLASHDeconv class keeps MSn-1 spectra deconvolution information for a certain period for precursor mass assignment in DeconvolvedSpectrum class. In case of FLASHIda runs, this precursor mass assignment is done by FLASHIda. Thus FLASHDeconv class simply parses the log file from FLASHIda runs and pass the parsed information to DeconvolvedSpectrum class.

See https://openms.de/FLASHDeconv for more information.

The command line parameters of this tool are:

FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FLASHDeconv.html
Version: 3.1.0-pre-FVdeploy-2025-01-12 Jan 12 2025, 12:57:41, Revision: 26f583c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite FLASHDeconv:
 + Jeong K, Kim J, Gaikwad M et al.. FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down 
   Proteomics. Cell Syst 2020 Feb 26;10(2):213-218.e6. doi:10.1016/j.cels.2020.01.003.

Usage:
  FLASHDeconv <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 <file>*                 Input file in mzML format.  (valid formats: 'mzML')
  -out <file>*                Default output tsv file containing deconvolved features (valid formats: 'tsv')
  -out_spec1 <file>           Output tsv file for deconvolved MS1 spectra. Use -out_spec2, ..., -out_spec4 
                              for MS2, ..., MS4 spectra. (valid formats: 'tsv')
  -out_mzml <file>            Output mzML file containing deconvolved spectra (for all MS levels). (valid 
                              formats: 'mzML')
  -out_quant <file>           Output tsv file with isobaric quantification results for MS2 spectra. (valid 
                              formats: 'tsv')
  -out_annotated_mzml <file>  Output annotated mzML file with monoisotopic mass, charge, and isotope index 
                              metadata for peaks. Unannotated peaks are also retained without metadata. (vali
                              d formats: 'mzML')
  -out_msalign1 <file>        Output msalign (TopFD and ProMex compatible) file for MS1 deconvolved spectra. 
                              Ensure filename ends with ms1.msalign for TopPIC GUI compatibility (e.g., resul
                              t_ms1.msalign; refer to TopPIC input formats). (valid formats: 'msalign')
  -out_feature1 <file>        Output feature file (TopFD compatible) for MS1 spectra. It is needed for TopPIC
                               feature intensity output (refer to TopPIC input formats). (valid formats: 'fea
                              ture')
  -keep_empty_out             Retain empty output files (e.g., *.tsv files with no features).
  -write_detail               Include detailed peak information (m/z, intensity, charge, isotope index) for 
                              each deconvolved mass in the output spectrum tsv files specified by out_spec* 
                              options.
                              
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)

The following configuration subsections are valid:
 - FD   FLASHDeconv algorithm parameters
 - SD   Spectral deconvolution parameters
 - ft   Feature tracing parameters
 - iq   Isobaric quantification parameters

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/doxygen/nightly/html/TOPP_FLASHDeconv.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+FLASHDeconvUltra-fast high-quality deconvolution enables online processing of top-down MS data

version3.1.0-pre-FVdeploy-2025-01-12 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FLASHDeconv'

in Input file in mzML format. input file*.mzML

out Default output tsv file containing deconvolved featuresoutput file*.tsv

out_spec1 Output tsv file for deconvolved MS1 spectra. Use -out_spec2, ..., -out_spec4 for MS2, ..., MS4 spectra.output file*.tsv

out_spec2 Output TSV files for deconvolved MS2 spectra.output file*.tsv

out_spec3 Output TSV files for deconvolved MS3 spectra.output file*.tsv

out_spec4 Output TSV files for deconvolved MS4 spectra.output file*.tsv

out_mzml Output mzML file containing deconvolved spectra (for all MS levels).output file*.mzML

out_quant Output tsv file with isobaric quantification results for MS2 spectra.output file*.tsv

out_annotated_mzml Output annotated mzML file with monoisotopic mass, charge, and isotope index metadata for peaks. Unannotated peaks are also retained without metadata.output file*.mzML

out_msalign1 Output msalign (TopFD and ProMex compatible) file for MS1 deconvolved spectra. Ensure filename ends with ms1.msalign for TopPIC GUI compatibility (e.g., result_ms1.msalign; refer to TopPIC input formats).output file*.msalign

out_msalign2 Output msalign (TopFD and ProMex compatible) file for MS2 deconvolved spectra. Ensure filename ends with ms2.msalign for TopPIC GUI compatibility (e.g., result_ms2.msalign; refer to TopPIC input formats).output file*.msalign

out_feature1 Output feature file (TopFD compatible) for MS1 spectra. It is needed for TopPIC feature intensity output (refer to TopPIC input formats).output file*.feature

out_feature2 Output feature file (TopFD compatible) for MS2 spectra. It is needed for TopPIC feature intensity output (refer to TopPIC input formats).output file*.feature

keep_empty_outfalse Retain empty output files (e.g., *.tsv files with no features).true, false

mzml_mass_charge0 Charge state of deconvolved masses in mzML output specified by -out_mzml.-1:1

write_detailfalse Include detailed peak information (m/z, intensity, charge, isotope index) for each deconvolved mass in the output spectrum tsv files specified by out_spec* options.true, false

min_mz-1.0 Specify the minimum m/z values for peaks considered during deconvolution. Negative values disable the threshold.

max_mz-1.0 Specify the maximum m/z values for peaks considered during deconvolution. Negative values disable the threshold.

min_rt-1.0 Specify the minimum retention time (in seconds) for spectra considered during deconvolution. Negative values disable the threshold.

max_rt-1.0 Specify the maximum retention time (in seconds) for spectra considered during deconvolution. Negative values disable the threshold.

max_ms_level-1 Set the maximum MS level (inclusive) for deconvolution. Negative values disable the threshold.

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

+++FDFLASHDeconv algorithm parameters

ida_log Provide the log file generated by FLASHIda (e.g., IDA*.log) for coupling with FLASHIda acquisition.

report_FDRfalse Generate q-values (approximate FDR) for deconvolved masses. Decoy masses are also reported which were used for FDR calculation. (Beta version)true, false

allowed_isotope_error0 Tolerance for isotope index errors when calculating FDR. For instance, setting a value of 2 permits the inclusion of up to 2 isotope errors as valid matches. Beta version.

use_RNA_averaginefalse Use the RNA (nucleotide) averagine model for deconvolution.true, false

precursor_MS1_window3 Number of MS1 spectra around each MS2 spectrum to search for precursor peaks when determining the MS2 precursors. For MS2 spectrum, the mass of precursor ion should be determined for better deconvolution and reliable identification. If the mass of precursor ion is not found in the immediately preceding MS1 spectrum, previous or next MS1 spectra may be used instead. This parameter determines up to how many MS1 spectra around each MS2 spectrum will be searched.1:∞

isolation_window5.0 Specify the isolation window width for precursor determination. Used when this information is absent in the mzML file.

merging_method0 Method for merging spectra before deconvolution. 0: No merging 1: Gaussian averaging per MS level, effective for Q-TOF datasets. For MSn (n > 1), only the spectra from the same precursor mass (subject to tolerance set by SD:tol) are averaged. 2: Block merging, combining all spectra into one per MS level (e.g., for NativeMS datasets).0:2

merging_min_ms_level1 Min MS level for merging1:∞

merging_max_ms_level2 Max MS level for merging1:∞

+++SDSpectral deconvolution parameters

tol[10.0, 10.0] PPM Tolerance for MS1, 2, ...: Specify the tolerance values in parts per million (ppm) using the this option. For example, -tol 10.0 5.0 sets the tolerance to 10.0 ppm for MS1 and 5.0 ppm for MS2. If a negative value (e.g., -1) is provided, the tolerance will be estimated automatically by a tolerance estimation algorithm.

min_mass50.0 Minimum mass (Da)

max_mass1.0e05 Maximum mass (Da)

min_charge1 Minimum charge state for MS1 spectra (can be negative for negative mode). For MSn (n > 1), minimum charge is fixed to 1.

max_charge100 Maximum charge state for spectra (can be negative for negative mode). Apart from min_charge, this option applies to all MS levelss.

precursor_charge0 Charge state of the target precursor. All precursor charge for MSn (n > 1) is fixed to this value. When precursor m/z is provided within the input mzML file or is specified using precursor_mz option, precursor mass is calculated accordingly.0:∞

precursor_mz0.0 Target precursor m/z value. This option must be used in combination with the -precursor_charge option; otherwise, it will be ignored. If the -precursor_charge option is specified but this option is not, the precursor m/z value from the input mzML file will be used as the default.0.0:∞

min_cos[0.85, 0.85] Cosine similarity thresholds between avg. and observed isotope pattern for MS1, 2, ...: e.g., -min_cos 0.3 0.6 to specify 0.3 and 0.6 for MS1 and MS2, respectively.

min_snr[1.0, 0.8] Minimum charge SNR (the SNR of the isotope pattern of a specific charge) thresholds for MS1, 2, ...: e.g., -min_snr 1.0 0.6 to specify 1.0 and 0.6 for MS1 and MS2, respectively.

+++ftFeature tracing parameters

mass_error_ppm-1.0 Specifies the mass error tolerance for feature tracing in ppm. When negative, the MS1 tolerance for deconvolution is used (e.g., 16 ppm is used when -SD:tol 16).

quant_methodarea Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.area, median, max_height

min_sample_rate0.1 Minimum fraction of scans along the feature trace that must contain a peak. To raise feature detection sensitivity, lower this value close to 0.

min_trace_length10.0 Minimum expected length of a mass trace (in seconds). Only for MS1 (or minimum MS level in the dataset) feature tracing. For MSn, all traces are kept regardless of this value.

max_trace_length-1.0 Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.

min_cos-1.0 Cosine similarity threshold between avg. and observed isotope pattern. When negative, MS1 cosine threshold for spectral deconvolution (set by -SD:min_cos will be used

+++iqIsobaric quantification parameters

typenone Specifies the isobaric quantification method used in the experiment.none, itraq4plex, itraq8plex, tmt10plex, tmt11plex, tmt16plex, tmt18plex, tmt6plex

isotope_correctiontrue Enable isotope correction (highly recommended).true, false

reporter_mz_tol2.0e-03 Specifies the m/z tolerance (in Th) for reporter ion detection.

only_fully_quantifiedfalse Restricts analysis to spectra that are fully quantified, meaning all channels have non-zero intensity reporter ions.true, false