FLASHDeconv

Options

version

Version of the tool that generated this parameters file.

in_log

log file generated by FLASHIda (IDA*.log). Only needed for coupling with FLASHIda acquisition

min_precursor_snr

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_charge

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_mz

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_charge

Charge state of deconvolved masses in mzml output (specified by out_mzml)

preceding_MS1_count

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.

write_detail

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.

max_MS_level

Maximum MS level (inclusive) for deconvolution.

forced_MS_level

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.

merging_method

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)

report_FDR

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.

use_RNA_averagine

If set to 1, RNA averagine model is used

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

tol

ppm tolerance for MS1, MS2, ...

min_mass

Minimum mass (Da)

max_mass

Maximum mass (Da)

min_charge

Minimum charge state for MS1 spectra (can be negative for negative mode)

max_charge

Maximum charge state for MS1 spectra (can be negative for negative mode)

min_mz

If set to positive value, minimum m/z to deconvolve.

max_mz

If set to positive value, maximum m/z to deconvolve.

min_rt

If set to positive value, minimum RT to deconvolve.

max_rt

If set to positive value, maximum RT to deconvolve.

isolation_window

Default isolation window with. If the input mzML file does not contain isolation window width information, this width will be used.

min_isotope_cosine

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_error

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_intensity

Intensity threshold

mass_error_ppm

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_method

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.

min_sample_rate

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_length

Minimum expected length of a mass trace (in seconds).

max_trace_length

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

Cosine similarity threshold between avg. and observed isotope pattern for mass features. if not set, controlled by -Algorithm:min_isotope_cosine_ option

Views

FLASHDeconv Std Output

The text sent to standard out during the execution of FLASHDeconv.

FLASHDeconv Error Output

The text sent to standard error during the execution of FLASHDeconv. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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