Package com.compomics.util.experiment.massspectrometry

Examples of com.compomics.util.experiment.massspectrometry.Charge

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        }

        // set the min/max precursor charge
        prideParametersReport += "<br><br><b>Min Precusor Charge:</b> ";
        if (minPrecursorCharge != null) {
            prideSearchParameters.setMinChargeSearched(new Charge(Charge.PLUS, minPrecursorCharge));
            prideParametersReport += minPrecursorCharge;
        } else {
            prideParametersReport += prideSearchParameters.getMinChargeSearched().value + " (default)";
        }
        prideParametersReport += "<br><b>Max Precusor Charge:</b> ";
        if (maxPrecursorCharge != null) {
            prideSearchParameters.setMaxChargeSearched(new Charge(Charge.PLUS, maxPrecursorCharge));
            prideParametersReport += maxPrecursorCharge;
        } else {
            prideParametersReport += prideSearchParameters.getMaxChargeSearched().value + " (default)";
        }
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                    PeptideFragmentIon peptideFragmentIon = (PeptideFragmentIon) ionMatch.ion;

                    if (peptideFragmentIon.getNeutralLosses().isEmpty()) {

                        //Q1
                        Charge charge = bestAssumption.getIdentificationCharge();
                        double theoreticPrecMz = (peptide.getMass() + charge.value * ElementaryIon.proton.getTheoreticMass()) / charge.value;
                        writer.write(theoreticPrecMz + SEPARATOR);

                        //Q3
                        double theoreticFragMz = ionMatch.ion.getTheoreticMz(charge.value);
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            }
        }
        if (fractionMolecularWeights != null) {
            updatedVersion.setFractionMolecularWeights(fractionMolecularWeights);
        }
        updatedVersion.setMaxChargeSearched(new Charge(Charge.PLUS, 4));
        updatedVersion.setMinChargeSearched(new Charge(Charge.PLUS, 2));
        updatedVersion.setMaxEValue(100.0);
        updatedVersion.setHitListLength(100);
        updatedVersion.setMinimalChargeForMultipleChargedFragments(new Charge(Charge.PLUS, 3));
        updatedVersion.setMaxPeptideLength(20);
        updatedVersion.setMinPeptideLength(6);
        updatedVersion.setEstimateCharge(true);
        updatedVersion.setRemovePrecursor(false);
        updatedVersion.setScalePrecursor(false);
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Related Classes of com.compomics.util.experiment.massspectrometry.Charge

  • eu.isas.peptideshaker.followup.SwathExport
  • eu.isas.peptideshaker.gui.pride.PrideReshakeGUI
  • eu.isas.peptideshaker.preferences.SearchParameters
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