Identifies peptide features in raw (i.e. profile) LC-MS data.
| pot. predecessor tools |  FeatureFinderRaw | pot. successor tools |
| FileConverter | IDMapper | |
| FileFilter |
FeatureFinderRaw is a tool for the identification of peptide features in profile LC-MS data.
Algorithm
The underlying algorithm of the tool is equivalent to that of SILACAnalyzer.
The command line parameters of this tool are:
INI file documentation of this tool:
Parameter Tuning
input:
- in [*.mzML] - LC-MS dataset to be analyzed
- ini [*.ini] - file containing all parameters (see discussion below)
standard output:
- out [*.consensusXML] - contains the list of identified peptides
optional output:
out_clusters [*.consensusXML] - contains the complete set of data points passing the filters
The results of an analysis can be easily visualized within TOPPView. Simply load *.consensusXML and *.featureXML as layers over the original *.mzML.
Parameters in section algorithm:
- allow_missing_peaks - Low intensity peaks might be missing from the isotopic pattern of some of the peptides. Specify if such peptides should be included in the analysis.
- rt_threshold - Upper bound for the retention time [s] over which a characteristic peptide elutes.
- rt_min - Lower bound for the retentions time [s].
- intensity_cutoff - Lower bound for the intensity of isotopic peaks in a SILAC pattern.
- intensity_correlation - Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.
- model_deviation - 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 ).