compute MASCOT evalue

src/input/mascot/mascotdatparser.cpp

@@ -29,6 +29,7 @@
 
 #include "mascotdatparser.h"
 #include "mimeparser.h"
+#include <cmath>
 #include <QDebug>
 #include <pappsomspp/pappsoexception.h>
 #include "../../core/peptidextp.h"
@@ -328,7 +329,7 @@ void MascotDatParser::parseSummaryLine(const QString & summary_line) {
         else if (index.startsWith("qmatch")) {
             unsigned int query_index = index.mid(6).toUInt();
             //_current_query.title = value;
-            _summary_list[query_index-1].match=value.toUInt();
+            _summary_list[query_index-1].match=value.toDouble();
         }
 //qplughole1=14.820890
         else if (index.startsWith("qplughole")) {
@@ -368,12 +369,18 @@ void MascotDatParser::saveQuery() {
         peptide_evidence.setExperimentalMass(_summary_list[_current_query.query_index-1].exp_mass);
         peptide_evidence.setRetentionTime(_current_query.rt);
 
-        peptide_evidence.setParam(PeptideEvidenceParam::mascot_macth_score,  QVariant(_summary_list[_current_query.query_index-1].match));
-
         peptide_evidence.setIdentificationDataSource( _p_identification_data_source);
         //parse and save
         for(PeptideLine & peptide_line:peptide_list) {
 
+            pappso::pappso_double ion_score = peptide_line.peptide_string_list.at(7).toDouble();
+            peptide_evidence.setParam(PeptideEvidenceParam::mascot_score,  QVariant(ion_score));
+
+            peptide_evidence.setEvalue(getEvalue(ion_score, _current_query.query_index, 0.05));
+
+            peptide_evidence.setParam(PeptideEvidenceParam::mascot_expectation_value,  QVariant(peptide_evidence.getEvalue()));
+
+
             QString peptide_str =peptide_line.peptide_string_list.at(4);
             if (!peptide_line.subst.isEmpty()) {
                 //q856_p9_subst=1,X,W
@@ -426,3 +433,8 @@ void MascotDatParser::saveQuery() {
 
     qDebug() << "MascotDatParser::saveQuery end";
 }
+
+pappso::pappso_double MascotDatParser::getEvalue(pappso::pappso_double ion_score, unsigned int query_index,  pappso::pappso_double confidence_interval) const {
+    double identity_threshold = 10.0 * std::log(_summary_list.at(query_index-1).match / (confidence_interval * 20.0)) / log(10);;
+    return (confidence_interval * pow(10, ((identity_threshold - ion_score) / 10)));
+}

src/input/mascot/mascotdatparser.h

@@ -48,6 +48,10 @@ private:
     void saveQuery();
     void saveAndClearPeptide();
     
+    
+    pappso::pappso_double getEvalue(pappso::pappso_double ion_score, unsigned int query_index, pappso::pappso_double confidence_interval = 0.05) const;
+
+    
     struct PeptideLine {
         unsigned int query_index=0;
         unsigned int peptide_index=0;
@@ -63,9 +67,9 @@ private:
         QString title;
     };
     struct SummaryLine {
-        unsigned int match=0;
+        pappso::pappso_double match=0; //qmatch, identity threshold
         pappso::pappso_double exp_mass=0;
-        pappso::pappso_double plug_hole=0;
+        pappso::pappso_double plug_hole=0; //qplughole, homology threshold
     };
 private:
     Project * _p_project;

src/utils/types.h

@@ -51,11 +51,13 @@ enum class IdentificationEngine: std::int8_t {
 };
 
 /** \def PeptideEvidenceParam peptide evidence specific parameters
- *
+ * is_a: MS:1001143 ! PSM-level search engine specific statistic
  */
 enum class PeptideEvidenceParam: std::int8_t {
-    tandem_hyperscore=0, ///< X!Tandem hyperscore
-    mascot_macth_score=1 ///< MASCOT match score
+    tandem_hyperscore=0, ///< X!Tandem hyperscore MS:1001331
+    tandem_expectation_value=1, ///< X!Tandem expectation value MS:1001330
+    mascot_score=2, ///< PSI-MS MS:1001171 mascot:score 56.16
+    mascot_expectation_value=3///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006
 };
 
 /** \def IdentificationEngineParam identification engine parameters