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required parameter

advanced parameter

+SILACAnalyzerDetermination of peak ratios in LC-MS data

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'SILACAnalyzer'

in Raw LC-MS data to be analyzed. (Profile data required. Will not work with centroided data!)input file*.mzML

out Set of all identified peptide groups (i.e. peptide pairs or triplets or singlets or ..). The m/z-RT positions correspond to the lightest peptide in each group.output file*.consensusXML

out_clusters Optional debug output containing data points passing all filters, hence belonging to a SILAC pattern. Points of the same colour correspond to the mono-isotopic peak of the lightest peptide in a pattern.output file*.consensusXML

out_features Optional output file containing the individual peptide features in 'out'.output file*.featureXML

out_mzq Optional output file of MzQuantML.output file*.mzq

out_filters Optional output file containing all points that passed the filters as txt. Suitable as input for 'in_filters' to perform clustering without preceding filtering process.output file*.consensusXML

in_filters Optional input file containing all points that passed the filters as txt. Use output from 'out_filters' to perform clustering only.input file*.consensusXML

out_debug Filename base for debug output.

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmParameters for the algorithm.

allow_missing_peaksfalse Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Should such peptides be included in the analysis?true,false

rt_threshold30 Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)0:∞

rt_min0 Lower bound for the retention time [s].0:∞

intensity_cutoff1000 Lower bound for the intensity of isotopic peaks in a SILAC pattern.0:∞

intensity_correlation0.7 Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.0:1

model_deviation3 Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation ).1:∞

+++labelsIsotopic labels that can be specified in section 'sample'.

Arg66.0201290268 Arg6 mass shift0:∞

Arg1010.0082686 Arg10 mass shift0:∞

Lys44.0251069836 Lys4 mass shift0:∞

Lys66.0201290268 Lys6 mass shift0:∞

Lys88.0141988132 Lys8 mass shift0:∞

dICPL44.025107 mass difference between isotope-coded protein labels ICPL 4 and ICPL 00:∞

dICPL66.020129 mass difference between isotope-coded protein labels ICPL 6 and ICPL 00:∞

dICPL1010.045236 mass difference between isotope-coded protein labels ICPL 10 and ICPL 00:∞

Methyl44.0202 Methyl4 mass shift0:∞

Methyl88.0202 Methyl8 mass shift0:∞

Methyl1212.0202 Methyl12 mass shift0:∞

Methyl1616.0202 Methyl16 mass shift0:∞

Methyl2424.0202 Methyl24 mass shift0:∞

Methyl3232.0202 Methyl32 mass shift0:∞

+++sampleParameters describing the sample and its labels.

labels[Lys8,Arg10] Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see 'advanced parameters', section 'labels'. If left empty the tool identifies singlets, i.e. acts as peptide feature finder.

charge2:4 Range of charge states in the sample, i.e. min charge : max charge.

missed_cleavages0 Maximum number of missed cleavages.0:∞

peaks_per_peptide3:5 Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks.