@@ -671,13 +671,24 @@ void RcppPwiz::addSpectrumList(MSData& msd,

     }

     // MSn - precursor:

     if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {

+      // Fill precursor data. This preserves the precursor data even if the

+      // precursor scan is not available (e.g. after MS level filtering).

+      spct.precursors.resize(1);

+      Precursor& prec = spct.precursors.front();

+      if (collisionEnergy[i] != 0) {

+	prec.activation.set(MS_collision_induced_dissociation);

+	prec.activation.set(MS_collision_energy, collisionEnergy[i],

+			    UO_electronvolt);

+      }

+      prec.selectedIons.resize(1);

+      prec.selectedIons[0].set(MS_selected_ion_m_z, precursorMZ[i], MS_m_z);

+      prec.selectedIons[0].set(MS_peak_intensity, precursorIntensity[i],

+			       MS_number_of_detector_counts);

+      prec.selectedIons[0].set(MS_charge_state, precursorCharge[i]);

       // Get the spectrumId of the precursor. Assuming that precursorScanNum is

       // linked to the acquisitionNum of the precursor.

       // This seems to be correct, since both the acquisitionNum and the

       // precursorNum are extracted from the respective spectrum's ID.

-      // Also, if we DON'T find the precursorScanNum among the acquisitionNum

-      // we skip adding the precursor data. Might be that the MS data has been

-      // filtered and the precursor scan is not provided.

       precursor_idx = -1;

       for (int j = 0; j < spctr_data.size(); j++) {

 	if (precursorScanNum[i] == acquisitionNum[j]) {

@@ -686,19 +697,7 @@ void RcppPwiz::addSpectrumList(MSData& msd,

 	}

       }

       if (precursor_idx >= 0) {

-	spct.precursors.resize(1);

-	Precursor& prec = spct.precursors.front();

 	prec.spectrumID = spectrumId[precursor_idx];

-	if (collisionEnergy[i] > 0) {

-	  prec.activation.set(MS_collision_induced_dissociation);

-	  prec.activation.set(MS_collision_energy, collisionEnergy[i],

-			      UO_electronvolt);

-	}

-	prec.selectedIons.resize(1);

-	prec.selectedIons[0].set(MS_selected_ion_m_z, precursorMZ[i], MS_m_z);

-	prec.selectedIons[0].set(MS_peak_intensity, precursorIntensity[i],

-				 MS_number_of_detector_counts);

-	prec.selectedIons[0].set(MS_charge_state, precursorCharge[i]);

       }

     }

     // [X] collisionEnergy