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FeatureFinderMultiplex

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Determination of peak ratios in LC-MS data

Web Documentation for 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
Overwrite 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 simulataneously. 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

Input Ports

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LC-MS dataset in either centroid or profile mode [mzML]

Output Ports

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Output file containing the individual peptide features. [featureXML]
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Optional output file containing all detected peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group. [consensusXML]
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Optional output file containing all peaks which have been associated with a peptide feature (and subsequently blacklisted). [mzML]

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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Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
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