@@ -101,6 +101,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )

     std::vector<double> experimentalMassToCharge;

     std::vector<double> calculatedMassToCharge;

     std::vector<std::string> seq;

+    std::vector<std::string> peptideRef;

     std::vector<int> modification;

     std::vector<bool> isDecoy;

     std::vector<bool> passThreshold;

@@ -127,6 +128,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )

 		experimentalMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->experimentalMassToCharge);

 		calculatedMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->calculatedMassToCharge);

 		seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->peptideSequence);

+		peptideRef.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->id);

 		modification.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->modification.size());

 		isDecoy.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->isDecoy);

 		pre.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->pre));

@@ -168,6 +170,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )

 	       Rcpp::_["experimentalMassToCharge"]	= experimentalMassToCharge,

 	       Rcpp::_["calculatedMassToCharge"]	= calculatedMassToCharge,

 	       Rcpp::_["sequence"]	= seq,

+	       Rcpp::_["peptideRef"]	= peptideRef,

 	       Rcpp::_["modNum"]	= modification,

 	       Rcpp::_["isDecoy"]	= isDecoy,

 	       Rcpp::_["post"]	= post,

@@ -187,6 +190,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )

     vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;

     vector<string> spectrumID;

     vector<string> seq;

+    vector<string> peptideRef;

     vector<string> name;

     vector<double> mass;

     vector<int> loc;

@@ -201,6 +205,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )

 		{

 		    spectrumID.push_back(spectrumIdResult[i]->spectrumID);

 		    seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->peptideSequence);

+		    peptideRef.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->id);

 		    name.push_back(cvTermInfo(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->cvParams[0].cvid).name);

 		    mass.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->monoisotopicMassDelta);

 		    loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->location);

@@ -212,6 +217,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )

     return Rcpp::DataFrame::create(

 	       Rcpp::_["spectrumID"]	= spectrumID,

 	       Rcpp::_["sequence"]	= seq,

+	       Rcpp::_["peptideRef"]	= peptideRef,

 	       Rcpp::_["name"]	= name,

 	       Rcpp::_["mass"]	= mass,

 	       Rcpp::_["location"]	= loc);

@@ -347,16 +353,16 @@ Rcpp::DataFrame RcppIdent::getSpecParams(  )

         }

         Rcpp::List res(score.size() + 1);

-        

+

         names.insert(names.begin(), "spectrumID");

-        

+

         res[0] = Rcpp::wrap(spectrumID);

-        

+

         for(size_t i = 0; i < score.size(); i++)

         {

             res[i + 1] = Rcpp::wrap(score[i]);

         }

-        

+

         res.attr("names") = names;

         Rcpp::DataFrame out(res);