OpenMS
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 FLASHDeconvAlgorithm 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: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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>

Options (mandatory options marked with '*'):
  -in <file>*                                                      Input file (mzML) (valid formats: 'mzML')
  -out <file>*                                                     Default output tsv file containing deconvo
                                                                   lved features (valid formats: 'tsv')
  -out_spec <file for MS1, file for MS2, ...>                      Output tsv files containing deconvolved 
                                                                   spectra (per MS level) (valid formats: 
                                                                   'tsv')
  -out_mzml <file>                                                 Output mzml file containing deconvolved 
                                                                   spectra (of all MS levels) (valid formats:
                                                                    'mzML')
  -out_annotated_mzml <file>                                       Output mzml file containing annotated spec
                                                                   tra. For each annotated peak, monoisotopic
                                                                    mass, charge, and isotope index are store
                                                                   d as meta data. Unannotated peaks are also
                                                                    copied as well without meta data. (valid 
                                                                   formats: 'mzML')
  -out_promex <file>                                               Output ms1ft (promex compatible) file cont
                                                                   aining deconvolved spectra. Only for MS1 
                                                                   level (valid formats: 'ms1ft')
  -out_topFD <file for MS1, file for MS2, ...>                     Output msalign (topFD compatible) files 
                                                                   containing deconvolved spectra (per MS 
                                                                   level). The file name for MSn should end 
                                                                   with msn.msalign to be able to be recogniz
                                                                   ed by TopPIC GUI. For example, -out_topFD 
                                                                   [name]_ms1.msalign [name]_ms2.msalign (val
                                                                   id formats: 'msalign')
  -out_topFD_feature <file for MS1, file for MS2, ...>             Output feature (topFD compatible) files 
                                                                   containing deconvolved features (per MS 
                                                                   level). The feature files are necessary 
                                                                   for TopPIC feature intensity output (valid
                                                                    formats: 'feature')
  -min_precursor_snr <SNR value>                                   Minimum precursor SNR (SNR within the prec
                                                                   ursor envelope range) for identification. 
                                                                   Similar to precursor interference level, 
                                                                   but far more stringent as it also consider
                                                                   s the isotope distribution shape of signal
                                                                   .When FLASHIda log file is used, this para
                                                                   meter is ignored. Applied only for topFD 
                                                                   msalign outputs. (default: '1.0')
  -target_precursor_charge <Target precursor charge>               Charge state of the target precursor. All 
                                                                   precursor charge is fixed to this value. 
                                                                   This parameter is useful for targeted stud
                                                                   ies where MS2 spectra are generated from 
                                                                   a fixed precursor (e.g., Native-MS). This 
                                                                   option also gives the maximum charge and 
                                                                   masses (together with precursor m/z) of 
                                                                   fragment ions, which overrides -Algorithm:
                                                                   max_charge and -Algorithm:max_mass. (defau
                                                                   lt: '0')
  -target_precursor_mz <m/z value>                                 Target precursor m/z value. This option 
                                                                   must be used with -target_precursor_charge
                                                                    option. Otherwise it will be ignored. If 
                                                                   -target_precursor_charge option is used 
                                                                   but this option is not used, the precursor
                                                                    m/z value written in MS2 spectra will be 
                                                                   used by default. Together with -target_pre
                                                                   cursor_charge, this option overrides -Algo
                                                                   rithm:max_mass. (default: '0.0')
  -mzml_mass_charge <0:uncharged 1: +1 charged -1: -1 charged>     Charge state of deconvolved masses in mzml
                                                                    output (specified by out_mzml) (default: 
                                                                   '0') (min: '-1' max: '1')
  -preceding_MS1_count <number>                                    Specifies the number of preceding MS1 spec
                                                                   tra for MS2 precursor determination. In 
                                                                   TDP, the precursor peak of a MS2 spectrum 
                                                                   may not belong to any deconvolved masses 
                                                                   in the MS1 spectrum immediately preceding 
                                                                   the MS2 spectrum. Increasing this paramete
                                                                   r to N allows for the search for the decon
                                                                   volved masses in the N preceding MS1 spect
                                                                   ra from the MS2 spectrum, increasing the 
                                                                   chance that its precursor is deconvolved. 
                                                                   (default: '3') (min: '1')
  -write_detail <1:true 0:false>                                   To write peak information per deconvolved 
                                                                   mass in detail or not in tsv files for 
                                                                   deconvolved spectra. If set to 1, all peak
                                                                    information (m/z, intensity, charge and 
                                                                   isotope index) per mass is reported. (defa
                                                                   ult: '0') (min: '0' max: '1')
  -merging_method <0: None 1: gaussian averaging 2: block method>  Method for spectra merging before deconvol
                                                                   ution. 0: No merging 1: Average gaussian 
                                                                   method to perform moving gaussian averagin
                                                                   g of spectra per MS level. Effective to 
                                                                   increase proteoform ID sensitivity (in 
                                                                   particular for Q-TOF datasets). 2: Block 
                                                                   method to perform merging of all spectra 
                                                                   into a single one per MS level (e.g., for 
                                                                   NativeMS datasets) (default: '0') (min: 
                                                                   '0' max: '2')
  -report_FDR <0: Do not report 1: report>                         Report qvalues (roughly, point-wise FDR) 
                                                                   for deconvolved masses in the tsv files 
                                                                   for deconvolved spectra. Dummy masses to 
                                                                   calculate qvalues and FDR are also reporte
                                                                   d. Beta version. (default: '0') (min: '0' 
                                                                   max: '1')

Algorithm:
  -Algorithm:tol <values>                                          Ppm tolerance for MS1, MS2, ...  (default:
                                                                    '[10.0 10.0 10.0]')
  -Algorithm:min_mass <value>                                      Minimum mass (Da) (default: '50.0')
  -Algorithm:max_mass <value>                                      Maximum mass (Da) (default: '1.0e05')
  -Algorithm:min_charge <number>                                   Minimum charge state for MS1 spectra (can 
                                                                   be negative for negative mode) (default: 
                                                                   '1')
  -Algorithm:max_charge <number>                                   Maximum charge state for MS1 spectra (can 
                                                                   be negative for negative mode) (default: 
                                                                   '100')
  -Algorithm:min_isotope_cosine <values>                           Cosine similarity thresholds between avg. 
                                                                   and observed isotope patterns for MS1, 2, 
                                                                   ... (e.g., -min_isotope_cosine 0.8 0.6 to 
                                                                   specify 0.8 and 0.6 for MS1 and MS2, respe
                                                                   ctively) (default: '[0.85 0.85 0.85]')

FeatureTracing:
  -FeatureTracing:mass_error_ppm <value>                           Feature tracing mass ppm tolerance. When 
                                                                   negative, MS1 tolerance for mass deconvolu
                                                                   tion will be used (e.g., 16 ppm is used 
                                                                   when -Algorithm:tol 16). (default: '-1.0')

  -FeatureTracing:min_sample_rate <value>                          Minimum fraction of scans along the featur
                                                                   e trace that must contain a peak. To raise
                                                                    feature detection sensitivity, lower this
                                                                    value close to 0. (default: '0.05')
  -FeatureTracing:min_trace_length <value>                         Minimum expected length of a mass trace 
                                                                   (in seconds). (default: '10.0')

                                                                   
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
+FLASHDeconvUltra-fast high-quality deconvolution enables online processing of top-down MS data
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FLASHDeconv'
in Input file (mzML)input file*.mzML
in_log log file generated by FLASHIda (IDA*.log). Only needed for coupling with FLASHIda acquisition
out Default output tsv file containing deconvolved featuresoutput file*.tsv
out_spec[] Output tsv files containing deconvolved spectra (per MS level)output file*.tsv
out_mzml Output mzml file containing deconvolved spectra (of all MS levels)output file*.mzML
out_annotated_mzml Output mzml file containing annotated spectra. For each annotated peak, monoisotopic mass, charge, and isotope index are stored as meta data. Unannotated peaks are also copied as well without meta data.output file*.mzML
out_promex Output ms1ft (promex compatible) file containing deconvolved spectra. Only for MS1 leveloutput file*.ms1ft
out_topFD[] Output msalign (topFD compatible) files containing deconvolved spectra (per MS level). The file name for MSn should end with msn.msalign to be able to be recognized by TopPIC GUI. For example, -out_topFD [name]_ms1.msalign [name]_ms2.msalignoutput file*.msalign
out_topFD_feature[] Output feature (topFD compatible) files containing deconvolved features (per MS level). The feature files are necessary for TopPIC feature intensity outputoutput file*.feature
min_precursor_snr1.0 Minimum precursor SNR (SNR within the precursor envelope range) for identification. Similar to precursor interference level, but far more stringent as it also considers the isotope distribution shape of signal.When FLASHIda log file is used, this parameter is ignored. Applied only for topFD msalign outputs.
target_precursor_charge0 Charge state of the target precursor. All precursor charge is fixed to this value. This parameter is useful for targeted studies where MS2 spectra are generated from a fixed precursor (e.g., Native-MS). This option also gives the maximum charge and masses (together with precursor m/z) of fragment ions, which overrides -Algorithm:max_charge and -Algorithm:max_mass.
target_precursor_mz0.0 Target precursor m/z value. This option must be used with -target_precursor_charge option. Otherwise it will be ignored. If -target_precursor_charge option is used but this option is not used, the precursor m/z value written in MS2 spectra will be used by default. Together with -target_precursor_charge, this option overrides -Algorithm:max_mass.
mzml_mass_charge0 Charge state of deconvolved masses in mzml output (specified by out_mzml)-1:1
preceding_MS1_count3 Specifies the number of preceding MS1 spectra for MS2 precursor determination. In TDP, the precursor peak of a MS2 spectrum may not belong to any deconvolved masses in the MS1 spectrum immediately preceding the MS2 spectrum. Increasing this parameter to N allows for the search for the deconvolved masses in the N preceding MS1 spectra from the MS2 spectrum, increasing the chance that its precursor is deconvolved.1:∞
write_detail0 To write peak information per deconvolved mass in detail or not in tsv files for deconvolved spectra. If set to 1, all peak information (m/z, intensity, charge and isotope index) per mass is reported.0:1
max_MS_level3 Maximum MS level (inclusive) for deconvolution.1:∞
forced_MS_level0 If set to an integer N, MS level of all spectra will be set to N regardless of original MS level. Useful when deconvolving datasets containing only MS2 spectra.0:∞
merging_method0 Method for spectra merging before deconvolution. 0: No merging 1: Average gaussian method to perform moving gaussian averaging of spectra per MS level. Effective to increase proteoform ID sensitivity (in particular for Q-TOF datasets). 2: Block method to perform merging of all spectra into a single one per MS level (e.g., for NativeMS datasets)0:2
report_FDR0 Report qvalues (roughly, point-wise FDR) for deconvolved masses in the tsv files for deconvolved spectra. Dummy masses to calculate qvalues and FDR are also reported. Beta version.0:1
use_RNA_averagine0 If set to 1, RNA averagine model is used0:1
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
+++Algorithm
tol[10.0, 10.0, 10.0] ppm tolerance for MS1, MS2, ...
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)
max_charge100 Maximum charge state for MS1 spectra (can be negative for negative mode)
min_mz-1.0 If set to positive value, minimum m/z to deconvolve.
max_mz-1.0 If set to positive value, maximum m/z to deconvolve.
min_rt-1.0 If set to positive value, minimum RT to deconvolve.
max_rt-1.0 If set to positive value, maximum RT to deconvolve.
isolation_window5.0 Default isolation window with. If the input mzML file does not contain isolation window width information, this width will be used.
min_isotope_cosine[0.85, 0.85, 0.85] Cosine similarity thresholds between avg. and observed isotope patterns for MS1, 2, ... (e.g., -min_isotope_cosine 0.8 0.6 to specify 0.8 and 0.6 for MS1 and MS2, respectively)
allowed_isotope_error1 Allowed isotope index error for decoy and qvalue report. If it is set to 1, for example, +-1 isotope errors are not counted as false. Beta version.
min_intensity0.0 Intensity threshold
+++FeatureTracing
mass_error_ppm-1.0 Feature tracing mass ppm tolerance. When negative, MS1 tolerance for mass deconvolution will be used (e.g., 16 ppm is used when -Algorithm: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_rate0.05 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).
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_isotope_cosine-1.0 Cosine similarity threshold between avg. and observed isotope pattern for mass features. if not set, controlled by -Algorithm:min_isotope_cosine_ option