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IDPosteriorErrorProbability

Tool to estimate the probability of peptide hits to be incorrectly assigned.

potential predecessor tools → IDPosteriorErrorProbability → potential successor tools
MascotAdapter (or other ID engines) ConsensusID
Experimental classes
This tool has not been tested thoroughly and might behave not as expected!

By default an estimation is performed using the (inverse) Gumbel distribution for incorrectly assigned sequences and a Gaussian distribution for correctly assigned sequences. The probabilities are calculated by using Bayes' law, similar to PeptideProphet. Alternatively, a second Gaussian distribution can be used for incorrectly assigned sequences. At the moment, IDPosteriorErrorProbability is able to handle X! Tandem, Mascot, MyriMatch and OMSSA scores.

No target/decoy information needs to be provided, since the model fits are done on the mixed distribution.

In order to validate the computed probabilities an optional plot output can be generated. There are two parameters for the plot: The scores are plotted in the form of bins. Each bin represents a set of scores in a range of '(highest_score - smallest_score) / number_of_bins' (if all scores have positive values). The midpoint of the bin is the mean of the scores it represents. The parameter 'out_plot' should be used to give the plot a unique name. Two files are created. One with the binned scores and one with all steps of the estimation. If parameter top_hits_only is set, only the top hits of each peptide identification are used for the estimation process. Additionally, if 'top_hits_only' is set, target/decoy information is available and a FalseDiscoveryRate run was performed previously, an additional plot will be generated with target and decoy bins ('out_plot' must not be empty). A peptide hit is assumed to be a target if its q-value is smaller than fdr_for_targets_smaller. The plots are saved as a Gnuplot file. An attempt is made to call Gnuplot, which will create a PDF file containing all steps of the estimation. If this fails, the user has to run Gnuplot manually - or adjust the PATH environment such that Gnuplot can be found and retry.

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:

For the parameters of the algorithm section see the algorithms documentation:
fit_algorithm