diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
index 386da27..70e7bf1 100644
--- a/src/main/java/proteomics/ECL2.java
+++ b/src/main/java/proteomics/ECL2.java
@@ -234,22 +234,19 @@ private static void saveTargetResult(List<FinalResultEntry> result, Map<String,
                 if (re.hit_type == 0) {
                     int link_site_1 = re.link_site_1;
                     int link_site_2 = re.link_site_2;
-                    String pro_1 = re.pro_id_1;
-                    if (re.pro_id_1.contains(";")) {
-                        pro_1 = re.pro_id_1.split(";")[0];
+                    List<String> proAnnotationList1 = new LinkedList<>();
+                    for (String s : re.pro_id_1.split(";")) {
+                        proAnnotationList1.add(pro_annotate_map.get(s));
                     }
-                    String pro_2 = re.pro_id_2;
-                    if (re.pro_id_2.contains(";")) {
-                        pro_2 = re.pro_id_2.split(";")[0];
+                    List<String> proAnnotationList2 = new LinkedList<>();
+                    for (String s : re.pro_id_2.split(";")) {
+                        proAnnotationList2.add(pro_annotate_map.get(s));
                     }
 
-                    String annotate_1 = pro_annotate_map.get(pro_1).replace(',', ';');
-                    String annotate_2 = pro_annotate_map.get(pro_2).replace(',', ';');
-
                     if (dev) {
-                        writer.write(re.scan_num + "," + re.spectrum_id + "," + re.spectrum_mz + "," + re.spectrum_mass + "," + re.peptide_mass + "," + re.rt + "," + re.C13_correction + "," + re.charge + "," + String.format(Locale.US, "%.4f", re.score) + "," + re.delta_c + "," + String.format(Locale.US, "%.2f", re.ppm) + "," + re.seq_1 + "-" + link_site_1 + "-" + re.seq_2 + "-" + link_site_2 + "," + re.pro_id_1 + "-" + re.pro_id_2 + ",\"" + annotate_1 + "\",\"" + annotate_2 + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + "," + String.format(Locale.US, "%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\",," + re.candidate_num + "," + re.point_count + "," + String.format(Locale.US, "%.4f", re.r_square) + "," + String.format(Locale.US, "%.4f", re.slope) + "," + String.format(Locale.US, "%.4f", re.intercept) + "," + re.start_idx + "," + re.end_idx + "," + String.format(Locale.US, "%.4f", re.chain_score_1) + "," + re.chain_rank_1 + "," + String.format(Locale.US, "%.4f", re.chain_score_2) + "," + re.chain_rank_2 + "\n");
+                        writer.write(re.scan_num + "," + re.spectrum_id + "," + re.spectrum_mz + "," + re.spectrum_mass + "," + re.peptide_mass + "," + re.rt + "," + re.C13_correction + "," + re.charge + "," + String.format(Locale.US, "%.4f", re.score) + "," + re.delta_c + "," + String.format(Locale.US, "%.2f", re.ppm) + "," + re.seq_1 + "-" + link_site_1 + "-" + re.seq_2 + "-" + link_site_2 + "," + re.pro_id_1 + "-" + re.pro_id_2 + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + "," + String.format(Locale.US, "%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\",," + re.candidate_num + "," + re.point_count + "," + String.format(Locale.US, "%.4f", re.r_square) + "," + String.format(Locale.US, "%.4f", re.slope) + "," + String.format(Locale.US, "%.4f", re.intercept) + "," + re.start_idx + "," + re.end_idx + "," + String.format(Locale.US, "%.4f", re.chain_score_1) + "," + re.chain_rank_1 + "," + String.format(Locale.US, "%.4f", re.chain_score_2) + "," + re.chain_rank_2 + "\n");
                     } else {
-                        writer.write(re.scan_num + "," + re.spectrum_id + "," + re.spectrum_mz + "," + re.spectrum_mass + "," + re.peptide_mass + "," + re.rt + "," +  re.C13_correction + "," + re.charge + "," + String.format(Locale.US, "%.4f", re.score) + "," + re.delta_c + "," + String.format(Locale.US, "%.2f", re.ppm) + "," + re.seq_1 + "-" + link_site_1 + "-" + re.seq_2 + "-" + link_site_2 + "," + re.pro_id_1 + "-" + re.pro_id_2 + ",\"" + annotate_1 + "\",\"" + annotate_2 + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + "," + String.format(Locale.US, "%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\"\n");
+                        writer.write(re.scan_num + "," + re.spectrum_id + "," + re.spectrum_mz + "," + re.spectrum_mass + "," + re.peptide_mass + "," + re.rt + "," +  re.C13_correction + "," + re.charge + "," + String.format(Locale.US, "%.4f", re.score) + "," + re.delta_c + "," + String.format(Locale.US, "%.2f", re.ppm) + "," + re.seq_1 + "-" + link_site_1 + "-" + re.seq_2 + "-" + link_site_2 + "," + re.pro_id_1 + "-" + re.pro_id_2 + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + "," + String.format(Locale.US, "%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\"\n");
                     }
                 }
             }
diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
index 5f3bdd2..a3e009d 100644
--- a/src/main/java/proteomics/Search/Search.java
+++ b/src/main/java/proteomics/Search/Search.java
@@ -257,19 +257,27 @@ public FinalResultEntry convertResultEntry(int scanNum, ResultEntry result_entry
         spectrum_mass += C13_Diff_num * 1.00335483f;
         float ppm = (spectrum_mass - theo_mass) * 1e6f / theo_mass;
 
-        String pro_1 = "";
+        Set<String> pro1Set = new TreeSet<>();
+        boolean isDecoy1 = false;
         for (String temp : seqProMap.get(chain_entry_1.seq.replaceAll("[^A-Znc]", ""))) {
-            pro_1 += temp + ";";
+            pro1Set.add(temp);
+            if (temp.startsWith("DECOY")) { // there is no overlapped peptide between target and decoy.
+                isDecoy1 = true;
+            }
         }
-        String pro_2 = "";
+        Set<String> pro2Set = new TreeSet<>();
+        boolean isDecoy2 = false;
         for (String temp : seqProMap.get(chain_entry_2.seq.replaceAll("[^A-Znc]", ""))) {
-            pro_2 += temp + ";";
+            pro2Set.add(temp);
+            if (temp.startsWith("DECOY")) { // there is no overlapped peptide between target and decoy.
+                isDecoy2 = true;
+            }
         }
 
         int hit_type; // 0 = T-T; 1 = D-D; 2 = T-D;
-        if (pro_1.startsWith("DECOY") && pro_2.startsWith("DECOY")) {
+        if (isDecoy1 && isDecoy2) {
             hit_type = 1;
-        } else if (!pro_1.startsWith("DECOY") && !pro_2.startsWith("DECOY")) {
+        } else if (!isDecoy1 && !isDecoy2) {
             hit_type = 0;
         } else {
             hit_type = 2;
@@ -305,7 +313,7 @@ public FinalResultEntry convertResultEntry(int scanNum, ResultEntry result_entry
         String final_seq_1 = addFixMod(chain_seq_1, result_entry.getLinkSite1());
         String final_seq_2 = addFixMod(chain_seq_2, result_entry.getLinkSite2());
 
-        return new FinalResultEntry(scanNum, result_entry.spectrum_id, rank, result_entry.charge, result_entry.spectrum_mz, result_entry.spectrum_mass, theo_mass, result_entry.rt, ppm, result_entry.getScore(), delta_c, final_seq_1, result_entry.getLinkSite1(), pro_1, final_seq_2, result_entry.getLinkSite2(), pro_2, cl_type, hit_type, C13_Diff_num, result_entry.getEValue(), result_entry.getScoreCount(), result_entry.getRSquare(), result_entry.getSlope(), result_entry.getIntercept(), result_entry.getStartIdx(), result_entry.getEndIdx(), result_entry.getChainScore1(), result_entry.getChainRank1(), result_entry.getChainScore2(), result_entry.getChainRank2(), result_entry.getCandidateNum(), cal_evalue, spectrumEntry.mgfTitle);
+        return new FinalResultEntry(scanNum, result_entry.spectrum_id, rank, result_entry.charge, result_entry.spectrum_mz, result_entry.spectrum_mass, theo_mass, result_entry.rt, ppm, result_entry.getScore(), delta_c, final_seq_1, result_entry.getLinkSite1(), String.join(";", pro1Set), final_seq_2, result_entry.getLinkSite2(), String.join(";", pro2Set), cl_type, hit_type, C13_Diff_num, result_entry.getEValue(), result_entry.getScoreCount(), result_entry.getRSquare(), result_entry.getSlope(), result_entry.getIntercept(), result_entry.getStartIdx(), result_entry.getEndIdx(), result_entry.getChainScore1(), result_entry.getChainRank1(), result_entry.getChainScore2(), result_entry.getChainRank2(), result_entry.getCandidateNum(), cal_evalue, spectrumEntry.mgfTitle);
     }
 
     private void linearScan(SpectrumEntry spectrumEntry, SparseVector xcorrPL, int specMaxBinIdx, ChainEntry chainEntry, int binInx, TreeMap<Integer, ChainResultEntry> binChainMap, List<DebugEntry> debugEntryList, Map<String, Double> devChainScoreMap) {