OpenMS
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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/release/3.3.0/html/TOPP_FLASHDeconv.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 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: