diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
index c193771..f673a32 100644
--- a/src/main/java/proteomics/ECL2.java
+++ b/src/main/java/proteomics/ECL2.java
@@ -240,9 +240,9 @@ private static void saveTargetResult(List<FinalResultEntry> result, Map<String,
                     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("%.4f", re.score) + "," + re.delta_c + "," + String.format("%.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("%E", re.e_value) : "-") + "," + String.format("%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\",," + re.candidate_num + "," + re.point_count + "," + String.format("%.4f", re.r_square) + "," + String.format("%.4f", re.slope) + "," + String.format("%.4f", re.intercept) + "," + re.start_idx + "," + re.end_idx + "," + String.format("%.4f", re.chain_score_1) + "," + re.chain_rank_1 + "," + String.format("%.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 + ",\"" + 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");
                     } 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("%.4f", re.score) + "," + re.delta_c + "," + String.format("%.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("%E", re.e_value) : "-") + "," + String.format("%.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 + ",\"" + annotate_1 + "\",\"" + annotate_2 + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + "," + String.format(Locale.US, "%.4f", re.qvalue) + ",\"" + re.mgfTitle + "\"\n");
                     }
                 }
             }
@@ -286,9 +286,9 @@ private static void saveDecoyResult(List<FinalResultEntry> result, Map<String, S
                     }
 
                     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("%.4f", re.score) + "," + re.delta_c + "," + String.format("%.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("%E", re.e_value) : "-") + ",\"" + re.mgfTitle + "\",," + re.candidate_num + "," + re.point_count + "," + String.format("%.4f", re.r_square) + "," + String.format("%.4f", re.slope) + "," + String.format("%.4f", re.intercept) + "," + re.start_idx + "," + re.end_idx + "," + String.format("%.4f", re.chain_score_1) + "," + re.chain_rank_1 + "," + String.format("%.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 + ",\"" + annotate_1 + "\",\"" + annotate_2 + "\"," + (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + ",\"" + 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("%.4f", re.score) + "," + re.delta_c + "," + String.format("%.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("%E", re.e_value) : "-") + ",\"" + 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 + ",\"" + annotate_1 + "\",\"" + annotate_2 + "\"," +  (cal_evalue ? String.format(Locale.US, "%E", re.e_value) : "-") + ",\"" + re.mgfTitle + "\"\n");
                     }
                 }
             }
diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
index d8a0971..6129b60 100644
--- a/src/main/java/proteomics/Index/BuildIndex.java
+++ b/src/main/java/proteomics/Index/BuildIndex.java
@@ -326,7 +326,7 @@ private Set<VarSequence> generateModSeq(String seq, Set<Short> modFreeListSites,
                     for (int i = 0; i < seq.length(); ++i) {
                         sb.append(seq.substring(i, i + 1));
                         if (idxBinaryModMassMap.containsKey(i)) {
-                            sb.append(String.format("[%.2f]", idxBinaryModMassMap.get(i).get(0)));
+                            sb.append(String.format(Locale.US, "[%.2f]", idxBinaryModMassMap.get(i).get(0)));
                         }
                     }
                     varSeqSet.add(new VarSequence(sb.toString(), linkSite, binaryModParam.hashCode()));
@@ -445,7 +445,7 @@ private Set<VarSequence> generateModSeqSub(String seq, int[] idxCombination, Map
             for (int i = 0; i < seq.length(); ++i) {
                 sb.append(seq.charAt(i));
                 if (localIdxModMassMap.containsKey(i)) {
-                    sb.append(String.format("[%.2f]", localIdxModMassMap.get(i)));
+                    sb.append(String.format(Locale.US, "[%.2f]", localIdxModMassMap.get(i)));
                 }
             }
             outputSet.add(new VarSequence(sb.toString(), linkSite, binaryModType));
diff --git a/src/main/java/proteomics/Search/CalEValue.java b/src/main/java/proteomics/Search/CalEValue.java
index faa42d9..8b1b9c6 100644
--- a/src/main/java/proteomics/Search/CalEValue.java
+++ b/src/main/java/proteomics/Search/CalEValue.java
@@ -9,6 +9,7 @@
 import java.io.BufferedWriter;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.util.Locale;
 import java.util.TreeMap;
 
 public class CalEValue {
@@ -67,7 +68,7 @@ public class CalEValue {
                 try (BufferedWriter writer = new BufferedWriter(new FileWriter(scan_num + ".evalue.csv"))) {
                     writer.write("histogram\n");
                     for (int i = 0; i < max_nonzero_idx; ++i) {
-                        writer.write(String.format("%d\n", score_histogram[i]));
+                        writer.write(String.format(Locale.US, "%d\n", score_histogram[i]));
                     }
                 } catch (IOException ex) {
                     logger.error(ex.getMessage());
@@ -188,12 +189,12 @@ public class CalEValue {
 
         if (ECL2.debug) {
             try (BufferedWriter writer = new BufferedWriter(new FileWriter(scan_num + ".evalue.csv"))) {
-                writer.write(String.format("histogram,survival,ln(survival),slope=%.4f,intercept=%.4f,rsquare=%.4f,start=%d,end=%d\n", optimal_slope, optimal_intercept, max_r_square, optimal_start_idx, null_end_idx));
+                writer.write(String.format(Locale.US, "histogram,survival,ln(survival),slope=%.4f,intercept=%.4f,rsquare=%.4f,start=%d,end=%d\n", optimal_slope, optimal_intercept, max_r_square, optimal_start_idx, null_end_idx));
                 for (int i = 0; i <= max_nonzero_idx; ++i) {
                     if (i < ln_survival_count_array.length) {
-                        writer.write(String.format("%d,%d,%.4f\n", score_histogram[i], survival_count_array[i], ln_survival_count_array[i]));
+                        writer.write(String.format(Locale.US, "%d,%d,%.4f\n", score_histogram[i], survival_count_array[i], ln_survival_count_array[i]));
                     } else {
-                        writer.write(String.format("%d,%d\n", score_histogram[i], survival_count_array[i]));
+                        writer.write(String.format(Locale.US, "%d,%d\n", score_histogram[i], survival_count_array[i]));
                     }
                 }
             } catch (IOException ex) {
diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java
index 11d7d48..0a39d48 100644
--- a/src/main/java/proteomics/Search/Search.java
+++ b/src/main/java/proteomics/Search/Search.java
@@ -209,7 +209,7 @@ ResultEntry doSearch(SpectrumEntry spectrumEntry, SparseVector xcorrPL, int spec
                 debugEntryList.sort(Comparator.reverseOrder());
                 writer.write("chain,link_site,mass,score\n");
                 for (DebugEntry t : debugEntryList) {
-                    writer.write(String.format("%s,%d,%f,%f\n", addFixMod(t.chain, t.link_site), t.link_site, t.mass, t.score));
+                    writer.write(String.format(Locale.US, "%s,%d,%f,%f\n", addFixMod(t.chain, t.link_site), t.link_site, t.mass, t.score));
                 }
             } catch (IOException ex) {
                 logger.error(ex.getMessage());
@@ -372,10 +372,10 @@ private String addFixMod(String seq, int linkSite) {
             if (i == linkSite) { // priority order: linkSite > fixMod > varMod
                 sb.append(aa.aa);
             } else if (Math.abs(fix_mod_map.get(aa.aa)) > 1e-6) {
-                sb.append(String.format("%c[%.2f]", aa.aa, fix_mod_map.get(aa.aa)));
+                sb.append(String.format(Locale.US, "%c[%.2f]", aa.aa, fix_mod_map.get(aa.aa)));
             } else {
                 if (Math.abs(aa.delta_mass) > 1e-6) {
-                    sb.append(String.format("%c[%.2f]", aa.aa, aa.delta_mass));
+                    sb.append(String.format(Locale.US, "%c[%.2f]", aa.aa, aa.delta_mass));
                 } else {
                     sb.append(aa.aa);
                 }
diff --git a/src/main/java/proteomics/Types/AA.java b/src/main/java/proteomics/Types/AA.java
index 60506a5..f19a1a2 100644
--- a/src/main/java/proteomics/Types/AA.java
+++ b/src/main/java/proteomics/Types/AA.java
@@ -1,5 +1,7 @@
 package proteomics.Types;
 
+import java.util.Locale;
+
 public class AA {
 
     public final char aa;
@@ -11,7 +13,7 @@ public AA(char aa, float delta_mass) {
         this.aa = aa;
         this.delta_mass = delta_mass;
         if (Math.abs(delta_mass) > 1e-6) {
-            toString = String.format("%c[%.2f]", aa, delta_mass);
+            toString = String.format(Locale.US, "%c[%.2f]", aa, delta_mass);
         } else {
             toString = String.valueOf(aa);
         }