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Store PeptideIndexer settings as metavalues in SearchParameters (OpenMS#8489)
* Initial plan * Add PeptideIndexer settings as metavalues in ProteinIdentification Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Extract metavalue keys as constants to improve maintainability Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Remove trailing whitespace from PeptideIndexing.h Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Use !empty() instead of size() > 0 for better readability Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Store PeptideIndexer settings in SearchParameters instead of ProteinIdentification Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Remove unnecessary static constants for metavalue keys Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> * Fix PeptideIndexing test and update test output files - Fix unit test to provide ProteinIdentification before running (the test was creating an empty prot_ids vector but expecting metavalues to be set - the code only updates existing ProteinIdentifications) - Update all PeptideIndexer TOPP test expected output files to include the new metavalues in SearchParameters 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Add PeptideIndexer settings to TOPP test expected output files (OpenMS#8509) Update expected output files to include PeptideIndexer settings that are now written to SearchParameters. This includes decoy_string, enzyme, enzyme_specificity, and related parameters. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com> Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
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‎src/openms/include/OpenMS/ANALYSIS/ID/PeptideIndexing.h‎

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@@ -90,7 +90,7 @@ namespace OpenMS
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{
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public:
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/// name of enzyme/specificity which signals that the enzyme/specificity should be taken from meta information
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static char const* const AUTO_MODE; /* = 'auto' */
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static char const* const AUTO_MODE; /* = 'auto' */
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/// Exit codes
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enum ExitCodes

‎src/openms/source/ANALYSIS/ID/PeptideIndexing.cpp‎

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@@ -821,6 +821,22 @@ PeptideIndexing::ExitCodes PeptideIndexing::run_(FASTAContainer<T>& proteins, st
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OPENMS_LOG_INFO << " orphaned proteins : " << stats_orphaned_proteins << (keep_unreferenced_proteins_ ? " (all kept)" : " (all removed)\n");
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OPENMS_LOG_INFO << "-----------------------------------" << std::endl;
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// Store PeptideIndexer settings in SearchParameters metavalues for documentation
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for (Size run_idx = 0; run_idx < prot_ids.size(); ++run_idx)
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{
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ProteinIdentification::SearchParameters search_parameters = prot_ids[run_idx].getSearchParameters();
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search_parameters.setMetaValue("PeptideIndexer:decoy_string", decoy_string_);
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search_parameters.setMetaValue("PeptideIndexer:decoy_string_position", prefix_ ? "prefix" : "suffix");
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search_parameters.setMetaValue("PeptideIndexer:enzyme", enzyme.getEnzymeName());
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search_parameters.setMetaValue("PeptideIndexer:enzyme_specificity", EnzymaticDigestion::NamesOfSpecificity[enzyme.getSpecificity()]);
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search_parameters.setMetaValue("PeptideIndexer:aaa_max", aaa_max_);
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search_parameters.setMetaValue("PeptideIndexer:mismatches_max", mm_max_);
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search_parameters.setMetaValue("PeptideIndexer:IL_equivalent", IL_equivalent_ ? "true" : "false");
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search_parameters.setMetaValue("PeptideIndexer:allow_nterm_protein_cleavage", allow_nterm_protein_cleavage_ ? "true" : "false");
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search_parameters.setMetaValue("PeptideIndexer:unmatched_action", names_of_unmatched[(Size)unmatched_action_]);
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search_parameters.setMetaValue("PeptideIndexer:missing_decoy_action", names_of_missing_decoy[(Size)missing_decoy_action_]);
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prot_ids[run_idx].setSearchParameters(search_parameters);
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}
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/// exit if no peptides were matched to decoy
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bool has_error = false;

‎src/tests/class_tests/openms/source/PeptideIndexing_test.cpp‎

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@@ -343,6 +343,64 @@ START_SECTION((ExitCodes run(std::vector<FASTAFile::FASTAEntry>& proteins, std::
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}
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END_SECTION
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START_SECTION((Test PeptideIndexer settings stored as metavalues in SearchParameters))
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{
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// Test that PeptideIndexer settings are stored as metavalues in SearchParameters
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PeptideIndexing pi;
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Param p = pi.getParameters();
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p.setValue("decoy_string", "DECOY_");
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p.setValue("decoy_string_position", "prefix");
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p.setValue("enzyme:name", "Trypsin");
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p.setValue("enzyme:specificity", "full");
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p.setValue("aaa_max", 2);
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p.setValue("mismatches_max", 1);
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p.setValue("IL_equivalent", "true");
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p.setValue("allow_nterm_protein_cleavage", "false");
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p.setValue("unmatched_action", "warn");
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p.setValue("missing_decoy_action", "warn");
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pi.setParameters(p);
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std::vector<FASTAFile::FASTAEntry> proteins = toFASTAVec(QStringList() << "PEPTIDER" << "DECOY_SEQUENCE");
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// Create a ProteinIdentification with an identifier that matches the PeptideIdentifications
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std::vector<ProteinIdentification> prot_ids(1);
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prot_ids[0].setIdentifier("test_run");
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// Create PeptideIdentifications with matching identifier
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PeptideIdentificationList pep_ids = toPepVec(QStringList() << "PEPTIDER");
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for (auto& pep_id : pep_ids)
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{
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pep_id.setIdentifier("test_run");
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}
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PeptideIndexing::ExitCodes r = pi.run(proteins, prot_ids, pep_ids);
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TEST_EQUAL(r, PeptideIndexing::EXECUTION_OK);
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// Check that metavalues are set correctly in SearchParameters
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const ProteinIdentification::SearchParameters& search_params = prot_ids[0].getSearchParameters();
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:decoy_string"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:decoy_string"), "DECOY_");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:decoy_string_position"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:decoy_string_position"), "prefix");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:enzyme"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:enzyme"), "Trypsin");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:enzyme_specificity"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:enzyme_specificity"), "full");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:aaa_max"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:aaa_max"), 2);
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:mismatches_max"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:mismatches_max"), 1);
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:IL_equivalent"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:IL_equivalent"), "true");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:allow_nterm_protein_cleavage"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:allow_nterm_protein_cleavage"), "false");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:unmatched_action"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:unmatched_action"), "warn");
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TEST_EQUAL(search_params.metaValueExists("PeptideIndexer:missing_decoy_action"), true);
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TEST_EQUAL(search_params.getMetaValue("PeptideIndexer:missing_decoy_action"), "warn");
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}
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END_SECTION
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/////////////////////////////////////////////////////////////
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/////////////////////////////////////////////////////////////

‎src/tests/topp/OpenNuXL_1_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-25T09:54:31" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-24" search_parameters_ref="SP_0" >

‎src/tests/topp/OpenNuXL_2_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-25T09:54:32" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-24" search_parameters_ref="SP_0" >

‎src/tests/topp/OpenNuXL_3_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-08T16:59:48" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-07" search_parameters_ref="SP_0" >

‎src/tests/topp/OpenNuXL_4_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-08T16:59:48" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-07" search_parameters_ref="SP_0" >

‎src/tests/topp/OpenNuXL_5_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-25T09:54:32" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-24" search_parameters_ref="SP_0" >

‎src/tests/topp/OpenNuXL_6_output.idXML‎

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<SearchParameters id="SP_0" db="/home/sachsenb/Development/OpenMS/src/tests/topp/OpenNuXL_1_input.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="2:5" enzyme="trypsin/p" missed_cleavages="2" precursor_peak_tolerance="1000000000" precursor_peak_tolerance_ppm="true" peak_mass_tolerance="20" peak_mass_tolerance_ppm="true" >
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<VariableModification name="Oxidation (M)" />
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<UserParam type="string" name="extra_features" value="missed_cleavages,NuXL:mass_error_p,NuXL:err,NuXL:total_loss_score,NuXL:modds,NuXL:immonium_score,NuXL:precursor_score,NuXL:MIC,NuXL:Morph,NuXL:total_MIC,NuXL:ladder_score,NuXL:sequence_score,NuXL:total_Morph,NuXL:total_HS,NuXL:tag_XLed,NuXL:tag_unshifted,NuXL:tag_shifted,NuXL:aminoacid_max_tag,NuXL:aminoacid_id_to_max_tag_ratio,nr_candidates,-ln(poisson),NuXL:explained_peak_fraction,NuXL:theo_peak_fraction,NuXL:wTop50,NuXL:marker_ions_score,NuXL:partial_loss_score,NuXL:pl_MIC,NuXL:pl_err,NuXL:pl_Morph,NuXL:pl_modds,NuXL:pl_pc_MIC,NuXL:pl_im_MIC,NuXL:isPhospho,NuXL:isXL,NuXL:score,isotope_error,variable_modifications,precursor_intensity_log10,NuXL:NA_MASS_z0,NuXL:NA_length,nucleotide_mass_tags,n_theoretical_peaks,NuXL:XL_U"/>
7+
<UserParam type="string" name="PeptideIndexer:decoy_string" value="DECOY_"/>
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<UserParam type="string" name="PeptideIndexer:decoy_string_position" value="prefix"/>
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<UserParam type="string" name="PeptideIndexer:enzyme" value="Trypsin/P"/>
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<UserParam type="string" name="PeptideIndexer:enzyme_specificity" value="full"/>
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<UserParam type="int" name="PeptideIndexer:aaa_max" value="3"/>
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<UserParam type="int" name="PeptideIndexer:mismatches_max" value="0"/>
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<UserParam type="string" name="PeptideIndexer:IL_equivalent" value="false"/>
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<UserParam type="string" name="PeptideIndexer:allow_nterm_protein_cleavage" value="true"/>
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<UserParam type="string" name="PeptideIndexer:unmatched_action" value="error"/>
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<UserParam type="string" name="PeptideIndexer:missing_decoy_action" value="silent"/>
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<UserParam type="string" name="feature_extractor" value="TOPP_PSMFeatureExtractor"/>
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</SearchParameters>
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<IdentificationRun date="2025-06-25T09:54:41" search_engine="OpenNuXL" search_engine_version="3.5.0-pre-feature-NuXL-2025-06-24" search_parameters_ref="SP_0" >

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