FeatureFinderMultiplex

Options

version

Version of the tool that generated this parameters file.

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)

labels

Labels used for labelling the samples. If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example [][Lys8,Arg10] ... SILAC [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC [Dimethyl0][Dimethyl6] ... Dimethyl [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL

charge

Range of charge states in the sample, i.e. min charge : max charge.

isotopes_per_peptide

Range of isotopes per peptide in the sample. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks.

rt_typical

Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)

rt_band

The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum. For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases.

rt_min

Lower bound for the retention time [s]. (Any peptides seen for a shorter time period are not reported.)

mz_tolerance

m/z tolerance for search of peak patterns.

mz_unit

Unit of the 'mz_tolerance' parameter.

intensity_cutoff

Lower bound for the intensity of isotopic peaks.

peptide_similarity

Two peptides in a multiplet are expected to have the same isotopic pattern. This parameter is a lower bound on their similarity.

averagine_similarity

The isotopic pattern of a peptide should resemble the averagine model at this m/z position. This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model.

averagine_similarity_scaling

Let x denote this scaling factor, and p the averagine similarity parameter. For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)

missed_cleavages

Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)

spectrum_type

Type of MS1 spectra in input mzML file. 'automatic' determines the spectrum type directly from the input mzML file.

averagine_type

The type of averagine to use, currently RNA, DNA or peptide

knock_out

Is it likely that knock-outs are present? (Supported for doublex, triplex and quadruplex experiments only.)

Arg6

Label:13C(6) | C(-6) 13C(6) | unimod #188

Arg10

Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267

Lys4

Label:2H(4) | H(-4) 2H(4) | unimod #481

Lys6

Label:13C(6) | C(-6) 13C(6) | unimod #188

Lys8

Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259

Leu3

Label:2H(3) | H(-3) 2H(3) | unimod #262

Dimethyl0

Dimethyl | H(4) C(2) | unimod #36

Dimethyl4

Dimethyl:2H(4) | 2H(4) C(2) | unimod #199

Dimethyl6

Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510

Dimethyl8

Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330

ICPL0

ICPL | H(3) C(6) N O | unimod #365

ICPL4

ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687

ICPL6

ICPL:13C(6) | H(3) 13C(6) N O | unimod #364

ICPL10

ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866

Views

FeatureFinderMultiplex Std Output

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

FeatureFinderMultiplex Error Output

The text sent to standard error during the execution of FeatureFinderMultiplex. (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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