FLASHDeconv

Options

version

Version of the tool that generated this parameters file.

keep_empty_out

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

mzml_mass_charge

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

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.

min_mz

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

max_mz

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

min_rt

Specify the minimum retention time (in minutes) for spectra considered during deconvolution. Negative values disable the threshold.

max_rt

Specify the maximum retention time (in minutes) for spectra considered during deconvolution. Negative values disable the threshold.

max_ms_level

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

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)

ida_log

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

report_FDR

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

allowed_isotope_error

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_averagine

Use the RNA (nucleotide) averagine model for deconvolution.

precursor_MS1_window

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.

isolation_window

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

merging_method

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).

merging_min_ms_level

Min MS level for merging

merging_max_ms_level

Max MS level for merging

tol

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_mass

Minimum mass (Da)

max_mass

Maximum mass (Da)

min_charge

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

max_charge

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

precursor_charge

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.

precursor_mz

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.

min_cos

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

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.

mass_error_ppm

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).

ion_mobility_tolerance

Allowed ion mobility deviation (in 1/k0).

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). 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

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

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

type

Specifies the isobaric quantification method used in the experiment.

isotope_correction

Enable isotope correction (highly recommended).

reporter_mz_tol

Specifies the m/z tolerance (in Th) for reporter ion detection.

only_fully_quantified

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

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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