Merge pull request OpenMS#8592 from OpenMS/copilot/fix-sps-ms3-workflow-exception

Handle MS2 spectra without corresponding MS3 in IsobaricWorkflow SPS-MS3 workflow

Author: jpfeuffer

src/topp/IsobaricWorkflow.cpp

@@ -576,6 +576,10 @@ class TOPPIsobaricWorkflow :
 
       channel_extractor.registerChannelsInOutputMap(cmap, mz_file);
 
+      // Collect peptide IDs without corresponding MS3 spectra (thread-safe collection)
+      // Note: unassigned_pep_ids is shared across threads; push_back is protected by critical section
+      PeptideIdentificationList unassigned_pep_ids;
+
       #pragma omp parallel for /*num_threads(inner_threads)*/
       for (int64_t pep_idx = 0; pep_idx < static_cast<int64_t>(pep_ids.size()); ++pep_idx)
       {
@@ -589,6 +593,23 @@ class TOPPIsobaricWorkflow :
             std::vector<std::pair<double,unsigned>> channel_qc(quant_method->getNumberOfChannels(), std::make_pair(std::numeric_limits<double>::quiet_NaN(), 0));
 
             auto [quant_spec_idx, id_spec_idx, ms1_spec_idx] = getSpecIdxs_(ms2spec_it->second, exp, has_ms3);
+            
+            // Check if MS3 spectrum is missing for MS2 spectrum
+            if (has_ms3 && quant_spec_idx == -1)
+            {
+              // Store peptide ID with file association for unassigned IDs
+              PeptideIdentification unassigned_pep = pep;
+              unassigned_pep.setIdentifier(ID_RUN_NAME_);
+              unassigned_pep.setMetaValue(Constants::UserParam::ID_MERGE_INDEX, i);
+              #pragma omp critical(unassigned_pep_ids_collection)
+              {
+                OpenMS_Log_warn << "MS2 spectrum " << spec_ref << " at index " << ms2spec_it->second 
+                                << " does not have a corresponding MS3 spectrum. Skipping quantification and adding to unassigned.\n";
+                unassigned_pep_ids.push_back(std::move(unassigned_pep));
+              }
+              continue;
+            }
+            
             auto [quant_purity, id_purity] = getPurities_(quant_spec_idx, id_spec_idx, ms1_spec_idx, exp, has_ms3, max_precursor_isotope_deviation, calc_id_purity, interpolate_precursor_purity);
 
             if (has_ms3 && exp[quant_spec_idx].getMSLevel() != 3)
@@ -628,6 +649,17 @@ class TOPPIsobaricWorkflow :
       }
       channel_extractor.printStatsWithMissing(qc);
 
+      // Add peptide IDs without MS3 spectra to unassigned IDs
+      if (!unassigned_pep_ids.empty())
+      {
+        OPENMS_LOG_INFO << "Adding " << unassigned_pep_ids.size() 
+                        << " peptide identifications without MS3 spectra to unassigned IDs." << std::endl;
+        auto& cmap_unassigned = cmap.getUnassignedPeptideIdentifications();
+        cmap_unassigned.insert(cmap_unassigned.end(), 
+                               std::make_move_iterator(unassigned_pep_ids.begin()), 
+                               std::make_move_iterator(unassigned_pep_ids.end()));
+      }
+
       // TODO if we want to support normalization, we either need to replace the quantifier with corrector and normalizer separately
       //  or init the normalizer from the quantifier settings.
       // But honestly, most downstream software can do it better, so I would not bother. Just export to mzTab and do it in R/python.