Examples with Enzyme com.compomics.util.experiment.biology.enzymes.Enzyme used on opensource projects

Example 1 with Enzyme

use of com.compomics.util.experiment.biology.enzymes.Enzyme in project peptide-shaker by compomics.

the class QCPanel method getPeptideDataset.

/**
 * Returns the dataset to use for the peptide QC plot.
 */
private void getPeptideDataset() {
    maxValue = Double.MIN_VALUE;
    SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
    if (peptideValidatedPsmsJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // values for the number of validated PSMs
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            double value = 0;
            for (long spectrumMatchKey : peptideMatch.getSpectrumMatchesKeys()) {
                if (progressDialog.isRunCanceled()) {
                    break;
                }
                SpectrumMatch spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumMatchKey);
                PSParameter spectrumParameter = (PSParameter) spectrumMatch.getUrParam(PSParameter.dummy);
                if (spectrumParameter.getMatchValidationLevel().isValidated() && !spectrumParameter.getHidden()) {
                    value = value + 1;
                }
            }
            if (value > maxValue) {
                maxValue = value;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(value);
                        } else {
                            validatedDoubtfulValues.add(value);
                        }
                    } else {
                        nonValidatedValues.add(value);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(value);
                } else {
                    nonValidatedDecoyValues.add(value);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    } else if (peptideMissedCleavagesJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // Values for the missed cleavages
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                Double value = null;
                DigestionParameters digestionParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getDigestionParameters();
                if (digestionParameters.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                    for (Enzyme enzyme : digestionParameters.getEnzymes()) {
                        int enzymeMissedCelavages = enzyme.getNmissedCleavages(peptideMatch.getPeptide().getSequence());
                        if (value == null || enzymeMissedCelavages < value) {
                            value = Double.valueOf(enzymeMissedCelavages);
                        }
                    }
                }
                if (value == null) {
                    value = 0.0;
                }
                if (value > 0) {
                    if (value > maxValue) {
                        maxValue = value;
                    }
                }
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(value);
                        } else {
                            validatedDoubtfulValues.add(value);
                        }
                    } else {
                        nonValidatedValues.add(value);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(value);
                } else {
                    nonValidatedDecoyValues.add(value);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    } else if (peptideLengthJRadioButton.isSelected()) {
        progressDialog.setPrimaryProgressCounterIndeterminate(false);
        progressDialog.setMaxPrimaryProgressCounter(peptideShakerGUI.getIdentification().getPeptideIdentification().size());
        progressDialog.setValue(0);
        // values for the peptide length
        validatedValues = new ArrayList<>();
        validatedDoubtfulValues = new ArrayList<>();
        nonValidatedValues = new ArrayList<>();
        validatedDecoyValues = new ArrayList<>();
        nonValidatedDecoyValues = new ArrayList<>();
        PeptideMatchesIterator peptideMatchesIterator = peptideShakerGUI.getIdentification().getPeptideMatchesIterator(progressDialog);
        PeptideMatch peptideMatch;
        while ((peptideMatch = peptideMatchesIterator.next()) != null) {
            if (progressDialog.isRunCanceled()) {
                break;
            }
            PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
            if (!peptideParameter.getHidden()) {
                double length = peptideMatch.getPeptide().getSequence().length();
                if (length > 0) {
                    if (length > maxValue) {
                        maxValue = length;
                    }
                }
                if (!PeptideUtils.isDecoy(peptideMatch.getPeptide(), sequenceProvider)) {
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        if (peptideParameter.getMatchValidationLevel() == MatchValidationLevel.confident) {
                            validatedValues.add(length);
                        } else {
                            validatedDoubtfulValues.add(length);
                        }
                    } else {
                        nonValidatedValues.add(length);
                    }
                } else if (peptideParameter.getMatchValidationLevel().isValidated()) {
                    validatedDecoyValues.add(length);
                } else {
                    nonValidatedDecoyValues.add(length);
                }
            }
            progressDialog.increasePrimaryProgressCounter();
        }
    }
}

Example 2 with Enzyme

use of com.compomics.util.experiment.biology.enzymes.Enzyme in project peptide-shaker by compomics.

the class InclusionListExport method exportInclusionList.

/**
 * Writes an inclusion list based on the validated PSMs of the validated
 * peptides of the validated proteins.
 *
 * @param destinationFile the file where to write the inclusion list
 * @param identification the identification object containing all matches
 * and match parameters
 * @param identificationFeaturesGenerator the identification features
 * generator calculating identification metrics on the fly
 * @param spectrumProvider the spectrum provider
 * @param proteinFilters the inclusion list protein filters
 * @param peptideFilters the inclusion list peptide filters
 * @param exportFormat the export format
 * @param searchParameters the identification parameters
 * @param rtWindow the window to use for retention time
 * @param waitingHandler waiting handler displaying progress to the user
 * (can be null)
 * @param filterPreferences the general filtering preferences of this
 * project
 *
 * @throws IOException thrown if an error occurred while writing the file
 */
public static void exportInclusionList(File destinationFile, Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator, SpectrumProvider spectrumProvider, ArrayList<Integer> proteinFilters, ArrayList<PeptideFilterType> peptideFilters, ExportFormat exportFormat, SearchParameters searchParameters, double rtWindow, WaitingHandler waitingHandler, FilterParameters filterPreferences) throws IOException {
    if (waitingHandler != null) {
        if (waitingHandler.isRunCanceled()) {
            return;
        }
        waitingHandler.setWaitingText("Inclusion List - Writing File. Please Wait...");
        waitingHandler.resetSecondaryProgressCounter();
        waitingHandler.setMaxSecondaryProgressCounter(identification.getProteinIdentification().size());
    }
    try (SimpleFileWriter writer = new SimpleFileWriter(destinationFile, false)) {
        ProteinMatchesIterator proteinMatchesIterator = identification.getProteinMatchesIterator(waitingHandler);
        ProteinMatch proteinMatch;
        while ((proteinMatch = proteinMatchesIterator.next()) != null) {
            PSParameter proteinParameter = (PSParameter) proteinMatch.getUrParam(PSParameter.dummy);
            if (!proteinFilters.contains(proteinParameter.getProteinInferenceGroupClass())) {
                ArrayList<Long> peptideMatches = new ArrayList<>();
                for (long peptideKey : proteinMatch.getPeptideMatchesKeys()) {
                    PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
                    PSParameter peptideParameter = (PSParameter) peptideMatch.getUrParam(PSParameter.dummy);
                    if (peptideParameter.getMatchValidationLevel().isValidated()) {
                        boolean passesFilter = true;
                        for (PeptideFilterType filterType : peptideFilters) {
                            String sequence = peptideMatch.getPeptide().getSequence();
                            if (filterType == PeptideFilterType.degenerated) {
                                if (peptideParameter.getProteinInferenceGroupClass() != PSParameter.NOT_GROUP) {
                                    passesFilter = false;
                                    break;
                                }
                            } else if (filterType == PeptideFilterType.miscleaved) {
                                Integer peptideMinMissedCleavages = null;
                                DigestionParameters digestionPreferences = searchParameters.getDigestionParameters();
                                if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
                                    for (Enzyme enzyme : digestionPreferences.getEnzymes()) {
                                        int tempMissedCleavages = enzyme.getNmissedCleavages(sequence);
                                        if (peptideMinMissedCleavages == null || tempMissedCleavages < peptideMinMissedCleavages) {
                                            peptideMinMissedCleavages = tempMissedCleavages;
                                        }
                                    }
                                }
                                if (peptideMinMissedCleavages != null && peptideMinMissedCleavages > 0) {
                                    passesFilter = false;
                                    break;
                                }
                            } else if (filterType == PeptideFilterType.reactive) {
                                if (sequence.contains("M") || sequence.contains("C") || sequence.contains("W") || sequence.contains("NG") || sequence.contains("DG") || sequence.contains("QG") || sequence.startsWith("N") || sequence.startsWith("Q")) {
                                    passesFilter = false;
                                    break;
                                }
                            }
                        }
                        if (passesFilter) {
                            peptideMatches.add(peptideKey);
                        }
                    }
                }
                if (!peptideMatches.isEmpty()) {
                    for (long peptideKey : peptideMatches) {
                        PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
                        ArrayList<SpectrumMatch> validatedPsms = new ArrayList<>(peptideMatch.getSpectrumCount());
                        ArrayList<Double> retentionTimes = new ArrayList<>(peptideMatch.getSpectrumCount());
                        for (long spectrumKey : peptideMatch.getSpectrumMatchesKeys()) {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                PSParameter spectrumParameter = (PSParameter) spectrumMatch.getUrParam(PSParameter.dummy);
                                if (spectrumParameter.getMatchValidationLevel().isValidated()) {
                                    validatedPsms.add(spectrumMatch);
                                    retentionTimes.add(spectrumProvider.getPrecursorRt(spectrumMatch.getSpectrumFile(), spectrumMatch.getSpectrumTitle()));
                                }
                            }
                        }
                        if (!validatedPsms.isEmpty()) {
                            for (SpectrumMatch spectrumMatch : validatedPsms) {
                                double precursorMz = spectrumProvider.getPrecursorMz(spectrumMatch.getSpectrumFile(), spectrumMatch.getSpectrumTitle());
                                String line = getInclusionListLine(spectrumMatch, retentionTimes, rtWindow, precursorMz, exportFormat, searchParameters);
                                writer.writeLine(line);
                            }
                        }
                    }
                }
            }
            if (waitingHandler != null) {
                if (waitingHandler.isRunCanceled()) {
                    return;
                }
                waitingHandler.increaseSecondaryProgressCounter();
            }
        }
    }
}

Example 3 with Enzyme

use of com.compomics.util.experiment.biology.enzymes.Enzyme in project peptide-shaker by compomics.

the class PepXmlExport method writeMsmsRunSummary.

/**
 * Writes the MS2 run summary section.
 *
 * @param sw the XML file writer
 * @param identification the identification object containing the
 * identification results
 * @param spectrumProvider the spectrum provider
 * @param identificationParameters the identification parameters
 * @param waitingHandler a waiting handler to display progress and allow
 * interrupting the process
 *
 * @throws IOException exception thrown whenever an error is encountered
 * while reading or writing a file
 */
private void writeMsmsRunSummary(SimpleXmlWriter sw, Identification identification, SpectrumProvider spectrumProvider, IdentificationParameters identificationParameters, WaitingHandler waitingHandler) throws IOException {
    if (waitingHandler != null) {
        waitingHandler.setSecondaryProgressCounterIndeterminate(false);
        // reset the progress bar
        waitingHandler.resetSecondaryProgressCounter();
        waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());
    }
    TreeSet<String> msFiles = new TreeSet<>(identification.getSpectrumIdentification().keySet());
    for (String spectrumFileName : msFiles) {
        StringBuilder runStart = new StringBuilder();
        runStart.append("<msms_run_summary");
        String filePath = spectrumProvider.getFilePaths().get(spectrumFileName);
        if (filePath != null) {
            String baseName = IoUtil.removeExtension(filePath);
            String extension = IoUtil.getExtension(new File(filePath));
            runStart.append(" base_name=\"").append(baseName).append("\" ");
            runStart.append("raw_data_type=\"").append(extension).append("\" ");
            runStart.append("raw_data=\"").append(extension).append("\"");
        }
        runStart.append(">");
        sw.writeLine(runStart.toString());
        DigestionParameters digestionPreferences = identificationParameters.getSearchParameters().getDigestionParameters();
        if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.enzyme) {
            for (Enzyme enzyme : digestionPreferences.getEnzymes()) {
                DigestionParameters.Specificity specificity = digestionPreferences.getSpecificity(enzyme.getName());
                writeEnzyme(sw, enzyme, specificity);
            }
        }
        writeSearchSummary(sw, identificationParameters);
        writeSpectrumQueries(sw, identification, spectrumProvider, identificationParameters, spectrumFileName, waitingHandler);
        sw.writeLineDecreasedIndent("</msms_run_summary>");
        if (waitingHandler != null && waitingHandler.isRunCanceled()) {
            break;
        }
    }
}

Example 4 with Enzyme

use of com.compomics.util.experiment.biology.enzymes.Enzyme in project peptide-shaker by compomics.

the class PeptideShakerMethods method getIdentificationSettings.

/**
 * Returns the identification settings details.
 *
 * @param searchParameters the search parameters
 *
 * @return the identification settings details
 */
public static String getIdentificationSettings(SearchParameters searchParameters) {
    StringBuilder text = new StringBuilder("The identification settings were as follows: ");
    DigestionParameters digestionPreferences = searchParameters.getDigestionParameters();
    switch(digestionPreferences.getCleavageParameter()) {
        case unSpecific:
            text.append("No cleavage specificity; ");
            break;
        case wholeProtein:
            text.append("No digestion; ");
            break;
        case enzyme:
            for (int i = 0; i < digestionPreferences.getEnzymes().size(); i++) {
                Enzyme enzyme = digestionPreferences.getEnzymes().get(i);
                String enzymeName = enzyme.getName();
                if (i > 0) {
                    if (digestionPreferences.getEnzymes().size() == 2) {
                        text.append(" and ");
                    } else {
                        text.append(", ");
                        if (i == digestionPreferences.getEnzymes().size() - 1) {
                            text.append("and ");
                        }
                    }
                }
                text.append(enzymeName).append(", ").append(digestionPreferences.getSpecificity(enzymeName)).append(", with a maximum of ").append(digestionPreferences.getnMissedCleavages(enzymeName)).append(" missed cleavages");
            }
            break;
        default:
            throw new UnsupportedOperationException("Cleavage of type " + digestionPreferences.getCleavageParameter() + " not supported.");
    }
    text.append(searchParameters.getPrecursorAccuracy()).append(" ").append(searchParameters.getPrecursorAccuracyType()).append(" as MS1 and ").append(searchParameters.getFragmentIonAccuracy()).append(" ").append(searchParameters.getFragmentAccuracyType()).append(" as MS2 tolerances; ");
    ModificationFactory ptmFactory = ModificationFactory.getInstance();
    ArrayList<String> fixedPtmsNames = searchParameters.getModificationParameters().getFixedModifications();
    if (!fixedPtmsNames.isEmpty()) {
        text.append("fixed modifications: ");
        for (int i = 0; i < fixedPtmsNames.size(); i++) {
            if (i > 0) {
                if (fixedPtmsNames.size() == 2) {
                    text.append(" and ");
                } else {
                    text.append(", ");
                    if (i == fixedPtmsNames.size() - 1) {
                        text.append("and ");
                    }
                }
            }
            String ptmName = fixedPtmsNames.get(i);
            Modification ptm = ptmFactory.getModification(ptmName);
            char sign = ptm.getRoundedMass() < 0 ? '-' : '+';
            text.append(ptmName).append(" (").append(sign).append(ptm.getRoundedMass()).append(" Da)");
        }
        text.append(", ");
    }
    ArrayList<String> variablePtmsNames = searchParameters.getModificationParameters().getVariableModifications();
    if (!variablePtmsNames.isEmpty()) {
        text.append(" variable modifications: ");
        for (int i = 0; i < variablePtmsNames.size(); i++) {
            if (i > 0) {
                if (fixedPtmsNames.size() == 2) {
                    text.append(" and ");
                } else {
                    text.append(", ");
                    if (i == fixedPtmsNames.size() - 1) {
                        text.append("and ");
                    }
                }
            }
            String ptmName = variablePtmsNames.get(i);
            Modification ptm = ptmFactory.getModification(ptmName);
            char sign = ptm.getRoundedMass() < 0 ? '-' : '+';
            text.append(ptmName).append(" (").append(sign).append(ptm.getRoundedMass()).append(" Da)");
        }
        text.append(", ");
    }
    ArrayList<String> refinementFixedPtmsNames = searchParameters.getModificationParameters().getRefinementFixedModifications();
    if (!refinementFixedPtmsNames.isEmpty()) {
        text.append("fixed modifications during refinement procedure: ");
        for (int i = 0; i < refinementFixedPtmsNames.size(); i++) {
            if (i > 0) {
                if (fixedPtmsNames.size() == 2) {
                    text.append(" and ");
                } else {
                    text.append(", ");
                    if (i == fixedPtmsNames.size() - 1) {
                        text.append("and ");
                    }
                }
            }
            String ptmName = refinementFixedPtmsNames.get(i);
            Modification ptm = ptmFactory.getModification(ptmName);
            char sign = ptm.getRoundedMass() < 0 ? '-' : '+';
            text.append(ptmName).append(" (").append(sign).append(ptm.getRoundedMass()).append(" Da)");
        }
        text.append(", ");
    }
    ArrayList<String> refinementVariablePtmsNames = searchParameters.getModificationParameters().getRefinementVariableModifications();
    if (!refinementVariablePtmsNames.isEmpty()) {
        text.append("variable modifications during refinement procedure: ");
        for (int i = 0; i < refinementVariablePtmsNames.size(); i++) {
            if (i > 0) {
                if (fixedPtmsNames.size() == 2) {
                    text.append(" and ");
                } else {
                    text.append(", ");
                    if (i == fixedPtmsNames.size() - 1) {
                        text.append("and ");
                    }
                }
            }
            String ptmName = refinementVariablePtmsNames.get(i);
            Modification ptm = ptmFactory.getModification(ptmName);
            char sign = ptm.getRoundedMass() < 0 ? '-' : '+';
            text.append(ptmName).append(" (").append(sign).append(ptm.getRoundedMass()).append(" Da)");
        }
    }
    text.append(". All algorithms specific settings are listed in the Certificate of Analysis available in the supplementary information.");
    return text.toString();
}

Example 5 with Enzyme

use of com.compomics.util.experiment.biology.enzymes.Enzyme in project peptide-shaker by compomics.

the class MzIdentMLExport method writeAnalysisProtocol.

/**
 * Write the analysis protocol.
 */
private void writeAnalysisProtocol() {
    writer.write(getCurrentTabSpace());
    writer.write("<AnalysisProtocolCollection>");
    writer.newLine();
    tabCounter++;
    // add spectrum identification protocol
    writer.write(getCurrentTabSpace());
    writer.write("<SpectrumIdentificationProtocol analysisSoftware_ref=\"ID_software\" id=\"SearchProtocol_1\">");
    writer.newLine();
    tabCounter++;
    // the search type
    writer.write(getCurrentTabSpace());
    writer.write("<SearchType>");
    writer.newLine();
    tabCounter++;
    writeCvTerm(new CvTerm("PSI-MS", "MS:1001083", "ms-ms search", null));
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</SearchType>");
    writer.newLine();
    // the search parameters
    SearchParameters searchParameters = identificationParameters.getSearchParameters();
    writer.write(getCurrentTabSpace());
    writer.write("<AdditionalSearchParams>");
    writer.newLine();
    tabCounter++;
    writeCvTerm(new CvTerm("PSI-MS", "MS:1001211", "parent mass type mono", null));
    writeCvTerm(new CvTerm("PSI-MS", "MS:1001256", "fragment mass type mono", null));
    switch(mzIdentMLVersion) {
        case v1_1:
            break;
        case v1_2:
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002492", "consensus scoring", null));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002490", "peptide-level scoring", null));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002497", "group PSMs by sequence with modifications", null));
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002491", "modification localization scoring", null));
            break;
        default:
            throw new UnsupportedOperationException("mzIdentML version " + mzIdentMLVersion.name + " not supported.");
    }
    // @TODO: list all search parameters from the search engines used?
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</AdditionalSearchParams>");
    writer.newLine();
    // the modifications
    writer.write(getCurrentTabSpace());
    writer.write("<ModificationParams>");
    writer.newLine();
    tabCounter++;
    // create the ptm index map
    switch(mzIdentMLVersion) {
        case v1_1:
            break;
        case v1_2:
            for (String modName : searchParameters.getModificationParameters().getAllModifications()) {
                Modification modification = modificationProvider.getModification(modName);
                Double modMass = modification.getMass();
                Integer index = modIndexMap.get(modMass);
                if (index == null) {
                    modIndexMap.put(modMass, modIndexMap.size());
                }
            }
            break;
        default:
            throw new UnsupportedOperationException("mzIdentML version " + mzIdentMLVersion.name + " not supported.");
    }
    // iterate and add the modifications
    for (String modName : searchParameters.getModificationParameters().getAllModifications()) {
        Modification modification = modificationProvider.getModification(modName);
        ModificationType modificationType = modification.getModificationType();
        double modMass = modification.getMass();
        String aminoAcidsAtTarget;
        if (modificationType == ModificationType.modaa || modificationType == ModificationType.modcaa_peptide || modificationType == ModificationType.modcaa_protein || modificationType == ModificationType.modnaa_peptide || modificationType == ModificationType.modnaa_protein) {
            StringBuilder sb = new StringBuilder();
            for (Character aa : modification.getPattern().getAminoAcidsAtTarget()) {
                sb.append(aa);
            }
            aminoAcidsAtTarget = sb.toString();
        } else {
            aminoAcidsAtTarget = ".";
        }
        writer.write(getCurrentTabSpace());
        writer.write("<SearchModification residues=\"");
        writer.write(aminoAcidsAtTarget);
        writer.write("\" massDelta=\"");
        writer.write(Double.toString(modification.getRoundedMass()));
        writer.write("\" fixedMod= \"");
        writer.write(Boolean.toString(searchParameters.getModificationParameters().getFixedModifications().contains(modName)));
        writer.write("\" >");
        writer.newLine();
        tabCounter++;
        // add modification specificity
        if (modificationType != ModificationType.modaa) {
            writer.write(getCurrentTabSpace());
            writer.write("<SpecificityRules>");
            writer.newLine();
            tabCounter++;
            switch(modificationType) {
                case modn_protein:
                case modnaa_protein:
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002057", "modification specificity protein N-term", null));
                    break;
                case modn_peptide:
                case modnaa_peptide:
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001189", "modification specificity peptide N-term", null));
                    break;
                case modc_protein:
                case modcaa_protein:
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1002058", "modification specificity protein C-term", null));
                    break;
                case modc_peptide:
                case modcaa_peptide:
                    writeCvTerm(new CvTerm("PSI-MS", "MS:1001190", "modification specificity peptide C-term", null));
                    break;
                default:
                    break;
            }
            tabCounter--;
            writer.write(getCurrentTabSpace());
            writer.write("</SpecificityRules>");
            writer.newLine();
        }
        // add the modification cv term
        CvTerm ptmCvTerm = modification.getUnimodCvTerm();
        if (ptmCvTerm != null) {
            writeCvTerm(ptmCvTerm);
        } else {
            // try PSI-MOD instead
            ptmCvTerm = modification.getPsiModCvTerm();
            if (ptmCvTerm != null) {
                writeCvTerm(ptmCvTerm);
            } else {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1001460", "unknown modification", null));
            }
        }
        // add modification type/index
        switch(mzIdentMLVersion) {
            case v1_1:
                break;
            case v1_2:
                Integer modIndex = modIndexMap.get(modMass);
                if (modIndex == null) {
                    throw new IllegalArgumentException("No index found for PTM " + modification.getName() + " of mass " + modMass + ".");
                }
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002504", "modification index", modIndex.toString()));
                break;
            default:
                throw new UnsupportedOperationException("mzIdentML version " + mzIdentMLVersion.name + " not supported.");
        }
        tabCounter--;
        writer.write(getCurrentTabSpace());
        writer.write("</SearchModification>");
        writer.newLine();
    }
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</ModificationParams>");
    writer.newLine();
    // Digestion
    DigestionParameters digestionPreferences = searchParameters.getDigestionParameters();
    if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.unSpecific) {
        writer.write(getCurrentTabSpace());
        writer.write("<Enzymes independent=\"false\">");
        writer.newLine();
        tabCounter++;
        writer.write(getCurrentTabSpace());
        writer.write("<Enzyme name=\"unspecific cleavage\">");
        writer.newLine();
        tabCounter++;
        writer.write(getCurrentTabSpace());
        writer.write("<EnzymeName>");
        writer.newLine();
        tabCounter++;
        CvTerm enzymeCvTerm = new CvTerm("PSI-MS", "MS:1001091", "unspecific cleavage", null);
        writeCvTerm(enzymeCvTerm);
        tabCounter--;
        writer.write(getCurrentTabSpace());
        writer.write("</EnzymeName>");
        writer.newLine();
        tabCounter--;
        writer.write(getCurrentTabSpace());
        writer.write("</Enzyme>");
        writer.newLine();
    } else if (digestionPreferences.getCleavageParameter() == DigestionParameters.CleavageParameter.wholeProtein) {
        writer.write(getCurrentTabSpace());
        writer.write("<Enzymes independent=\"false\">");
        writer.newLine();
        tabCounter++;
        writer.write(getCurrentTabSpace());
        writer.write("<Enzyme name=\"NoEnzyme\">");
        writer.newLine();
        tabCounter++;
        writer.write(getCurrentTabSpace());
        writer.write("<EnzymeName>");
        writer.newLine();
        tabCounter++;
        CvTerm enzymeCvTerm = new CvTerm("PSI-MS", "MS:1001955", "NoEnzyme", null);
        writeCvTerm(enzymeCvTerm);
        tabCounter--;
        writer.write(getCurrentTabSpace());
        writer.write("</EnzymeName>");
        writer.newLine();
        tabCounter--;
        writer.write(getCurrentTabSpace());
        writer.write("</Enzyme>");
        writer.newLine();
    } else {
        ArrayList<Enzyme> enzymes = digestionPreferences.getEnzymes();
        writer.write(getCurrentTabSpace());
        writer.write("<Enzymes independent=\"");
        writer.write(Boolean.toString(enzymes.size() > 1));
        writer.write("\">");
        writer.newLine();
        tabCounter++;
        for (Enzyme enzyme : enzymes) {
            String enzymeName = enzyme.getName();
            writer.write(getCurrentTabSpace());
            writer.write("<Enzyme missedCleavages=\"");
            writer.write(Integer.toString(digestionPreferences.getnMissedCleavages(enzymeName)));
            writer.write("\" semiSpecific=\"");
            writer.write(Boolean.toString(digestionPreferences.getSpecificity(enzymeName) == DigestionParameters.Specificity.semiSpecific));
            writer.write("\" ");
            // + "cTermGain=\"OH\" " // Element formula gained at CTerm
            // + "nTermGain=\"H\" " // Element formula gained at NTerm
            // @TODO: add <SiteRegexp><![CDATA[(?<=[KR])(?!P)]]></SiteRegexp>?
            writer.write("id=\"Enz1\" name=\"");
            writer.write(enzyme.getName());
            writer.write("\">");
            writer.newLine();
            tabCounter++;
            writer.write(getCurrentTabSpace());
            writer.write("<EnzymeName>");
            writer.newLine();
            tabCounter++;
            CvTerm enzymeCvTerm = enzyme.getCvTerm();
            if (enzymeCvTerm != null) {
                writeCvTerm(enzymeCvTerm);
            } else {
                writeUserParam(enzyme.getName());
            }
            tabCounter--;
            writer.write(getCurrentTabSpace());
            writer.write("</EnzymeName>");
            writer.newLine();
            tabCounter--;
            writer.write(getCurrentTabSpace());
            writer.write("</Enzyme>");
            writer.newLine();
            tabCounter--;
        }
    }
    writer.write(getCurrentTabSpace());
    writer.write("</Enzymes>");
    writer.newLine();
    // fragment tolerance
    writer.write(getCurrentTabSpace());
    writer.write("<FragmentTolerance>");
    writer.newLine();
    tabCounter++;
    String fragmentIonToleranceUnit;
    String unitAccession;
    switch(searchParameters.getFragmentAccuracyType()) {
        case DA:
            fragmentIonToleranceUnit = "dalton";
            unitAccession = "UO:0000221";
            break;
        case PPM:
            fragmentIonToleranceUnit = "parts per million";
            unitAccession = "UO:0000169";
            break;
        default:
            throw new UnsupportedOperationException("CV term not implemented for fragment accuracy in " + searchParameters.getFragmentAccuracyType() + ".");
    }
    writer.write(getCurrentTabSpace());
    writer.write("<cvParam accession=\"MS:1001412\" cvRef=\"PSI-MS\" unitCvRef=\"UO\" unitName=\"");
    writer.write(fragmentIonToleranceUnit);
    writer.write("\" unitAccession=\"");
    writer.write(unitAccession);
    writer.write("\" value=\"");
    writer.write(Double.toString(searchParameters.getFragmentIonAccuracy()));
    writer.write("\" ");
    writer.write("name=\"search tolerance plus value\" />");
    writer.newLine();
    writer.write(getCurrentTabSpace());
    writer.write("<cvParam accession=\"MS:1001413\" cvRef=\"PSI-MS\" unitCvRef=\"UO\" unitName=\"");
    writer.write(fragmentIonToleranceUnit);
    writer.write("\" unitAccession=\"");
    writer.write(unitAccession);
    writer.write("\" value=\"");
    writer.write(Double.toString(searchParameters.getFragmentIonAccuracy()));
    writer.write("\" name=\"search tolerance minus value\" />");
    writer.newLine();
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</FragmentTolerance>");
    writer.newLine();
    // precursor tolerance
    writer.write(getCurrentTabSpace());
    writer.write("<ParentTolerance>");
    writer.newLine();
    tabCounter++;
    String precursorIonToleranceUnit;
    switch(searchParameters.getPrecursorAccuracyType()) {
        case DA:
            precursorIonToleranceUnit = "dalton";
            break;
        case PPM:
            precursorIonToleranceUnit = "parts per million";
            break;
        default:
            throw new UnsupportedOperationException("CV term not implemented for precursor accuracy in " + searchParameters.getFragmentAccuracyType() + ".");
    }
    writer.write(getCurrentTabSpace());
    writer.write("<cvParam accession=\"MS:1001412\" cvRef=\"PSI-MS\" unitCvRef=\"UO\" unitName=\"");
    writer.write(precursorIonToleranceUnit);
    writer.write("\" unitAccession=\"UO:0000169\" value=\"");
    writer.write(Double.toString(searchParameters.getPrecursorAccuracy()));
    writer.write("\" name=\"search tolerance plus value\" />");
    writer.newLine();
    writer.write(getCurrentTabSpace());
    writer.write("<cvParam accession=\"MS:1001413\" cvRef=\"PSI-MS\" unitCvRef=\"UO\" unitName=\"");
    writer.write(precursorIonToleranceUnit);
    writer.write("\" unitAccession=\"UO:0000169\" value=\"");
    writer.write(Double.toString(searchParameters.getPrecursorAccuracy()));
    writer.write("\" name=\"search tolerance minus value\" />");
    tabCounter--;
    writer.newLine();
    writer.write(getCurrentTabSpace());
    writer.write("</ParentTolerance>");
    writer.newLine();
    // thresholds
    writer.write(getCurrentTabSpace());
    writer.write("<Threshold>");
    writer.newLine();
    tabCounter++;
    boolean targetDecoy = identificationParameters.getFastaParameters().isTargetDecoy();
    if (!targetDecoy) {
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));
    } else {
        // Initial global thresholds
        IdMatchValidationParameters idMatchValidationPreferences = identificationParameters.getIdValidationParameters();
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "peptide sequence-level global FDR", Double.toString(Util.roundDouble(idMatchValidationPreferences.getDefaultPeptideFDR(), CONFIDENCE_DECIMALS))));
        writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(idMatchValidationPreferences.getDefaultPsmFDR(), CONFIDENCE_DECIMALS))));
        ModificationLocalizationParameters ptmScoringPreferences = identificationParameters.getModificationLocalizationParameters();
        if (ptmScoringPreferences.isProbabilisticScoreCalculation()) {
            if (ptmScoringPreferences.getSelectedProbabilisticScore() == ModificationLocalizationScore.PhosphoRS) {
                writeCvTerm(new CvTerm("PSI-MS", "MS:1002567", "phosphoRS score threshold", Double.toString(ptmScoringPreferences.getProbabilisticScoreThreshold())));
            }
        }
        writeCvTerm(new CvTerm("PSI-MS", "MS:1002557", "D-Score threshold", Double.toString(identificationParameters.getModificationLocalizationParameters().getDScoreThreshold())));
    // @TODO: add peptide and psm level annotation
    // // peptideshaker maps
    // PSMaps psMaps = new PSMaps();
    // psMaps = (PSMaps) identification.getUrParam(psMaps);
    // 
    // // peptide level threshold
    // PeptideSpecificMap peptideSpecificMap = psMaps.getPeptideSpecificMap();
    // ArrayList<String> peptideGroupsKeys = peptideSpecificMap.getKeys();
    // 
    // for (String key : peptideGroupsKeys) { // @TODO: find a way of annotating all thresholds..?
    // TargetDecoyMap targetDecoyMap = peptideSpecificMap.getTargetDecoyMap(key);
    // TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
    // double threshold = targetDecoyResults.getUserInput() / 100;
    // int thresholdType = targetDecoyResults.getInputType();
    // if (peptideGroupsKeys.size() > 1) {
    // String peptideClass = PeptideSpecificMap.getKeyName(searchParameters.getModificationProfile(), key);
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002544", "PeptideShaker peptide confidence type", peptideClass)); // peptide confidence type
    // }
    // if (thresholdType == 0) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002463", "distinct peptide-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
    // } else if (targetDecoyResults.getInputType() == 1) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1001364", "peptide sequence-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
    // } else if (targetDecoyResults.getInputType() == 2) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002462", "distinct peptide-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
    // }
    // }
    // 
    // // psm level threshold
    // ArrayList<Integer> chargesWithFileSpecificity = new ArrayList<Integer>();
    // PsmSpecificMap psmSpecificMap = psMaps.getPsmSpecificMap();
    // 
    // for (Integer charge : psmSpecificMap.getPossibleCharges()) {
    // for (String file : psmSpecificMap.getFilesAtCharge(charge)) {
    // if (!psmSpecificMap.isFileGrouped(charge, file)) { // @TODO: find a way of annotating all thresholds..?
    // chargesWithFileSpecificity.add(charge);
    // TargetDecoyMap targetDecoyMap = psMaps.getPsmSpecificMap().getTargetDecoyMap(charge, file);
    // TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
    // double threshold = targetDecoyResults.getUserInput() / 100;
    // int thresholdType = targetDecoyResults.getInputType();
    // String psmClass = "Charge " + charge + " of file " + file; // @TODO: annotate class?
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002543", "PeptideShaker PSM confidence type", "???")); // psm confidence type
    // if (thresholdType == 0) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
    // } else if (targetDecoyResults.getInputType() == 1) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
    // } else if (targetDecoyResults.getInputType() == 2) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
    // }
    // }
    // }
    // }
    // 
    // //@TODO: set the PSM group label
    // for (int charge : psmSpecificMap.getChargesFromGroupedFiles()) {
    // int correctedCharge = psmSpecificMap.getCorrectedCharge(charge);
    // if (correctedCharge == charge) {
    // TargetDecoyMap targetDecoyMap = psMaps.getPsmSpecificMap().getTargetDecoyMap(charge, null);
    // TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
    // double threshold = targetDecoyResults.getUserInput() / 100;
    // int thresholdType = targetDecoyResults.getInputType();
    // // @TODO: check the cv terms used!!!
    // if (thresholdType == 0) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002465", "PSM-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // confidence
    // } else if (targetDecoyResults.getInputType() == 1) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002350", "PSM-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FDR
    // } else if (targetDecoyResults.getInputType() == 2) {
    // writeCvTerm(new CvTerm("PSI-MS", "MS:1002464", "PSM-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS)))); // FNR
    // }
    // }
    // }
    // 
    // // @TODO: re-add psm ptm thresholds
    // PsmPTMMap psmPTMMap = psMaps.getPsmPTMMap();
    // if (psmPTMMap != null) { // backward compatibility: information only present in versions 0.28.2 and later
    // for (Double ptmMass : psmPTMMap.getModificationsScored()) {
    // for (int mapKey : psmPTMMap.getKeys(ptmMass).keySet()) {
    // TargetDecoyMap targetDecoyMap = psmPTMMap.getTargetDecoyMap(ptmMass, mapKey);
    // TargetDecoyResults targetDecoyResults = targetDecoyMap.getTargetDecoyResults();
    // double threshold = targetDecoyResults.getUserInput() / 100;
    // int thresholdType = targetDecoyResults.getInputType(); // For now only FDR is implemented but others will follow after my next transatlantic flight :)
    // String ptmClass = "Modification of mass " + ptmMass;
    // //@TODO: find cv terms
    // }
    // }
    // }
    // @TODO: one for ptm scores, one per ptm per charge state per file
    // match quality thresholds
    // @TODO: match quality thresholds?? some are per file...
    }
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</Threshold>");
    writer.newLine();
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</SpectrumIdentificationProtocol>");
    writer.newLine();
    // add ProteinDetectionProtocol
    writer.write(getCurrentTabSpace());
    writer.write("<ProteinDetectionProtocol analysisSoftware_ref=\"ID_software\" id=\"PeptideShaker_1\">");
    writer.newLine();
    tabCounter++;
    // br.write(getCurrentTabSpace() + "<AnalysisParams>" + lineBreak);
    // tabCounter++;
    // @TODO: add cv terms? (children of MS:1001302)
    // tabCounter--;
    // br.write(getCurrentTabSpace() + "</AnalysisParams>" + lineBreak);
    // protein level threshold
    writer.write(getCurrentTabSpace());
    writer.write("<Threshold>");
    writer.newLine();
    tabCounter++;
    if (!targetDecoy) {
        writeCvTerm(new CvTerm("PSI-MS", "MS:1001494", "no threshold", null));
    } else {
        PSMaps psMaps = new PSMaps();
        psMaps = (PSMaps) identification.getUrParam(psMaps);
        TargetDecoyMap proteinMap = psMaps.getProteinMap();
        TargetDecoyResults proteinTargetDecoyResults = proteinMap.getTargetDecoyResults();
        double threshold = proteinTargetDecoyResults.getUserInput() / 100;
        int thresholdType = proteinTargetDecoyResults.getInputType();
        if (thresholdType == 0) {
            // confidence
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002461", "protein group-level global confidence", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS))));
        } else if (proteinTargetDecoyResults.getInputType() == 1) {
            // FDR
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002369", "protein group-level global FDR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS))));
        } else if (proteinTargetDecoyResults.getInputType() == 2) {
            // FNR
            writeCvTerm(new CvTerm("PSI-MS", "MS:1002460", "protein group-level global FNR", Double.toString(Util.roundDouble(threshold, CONFIDENCE_DECIMALS))));
        }
    }
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</Threshold>");
    writer.newLine();
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</ProteinDetectionProtocol>");
    writer.newLine();
    tabCounter--;
    writer.write(getCurrentTabSpace());
    writer.write("</AnalysisProtocolCollection>");
    writer.newLine();
}