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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/3.2.0/html/TOPP_FLASHDeconv.html
Version: 3.2.0 Nov 26 2024, 13:16:38, Revision: 962e60f
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:
1.9.1