diff --git a/ProteoFileReader.pyc b/ProteoFileReader.pyc
new file mode 100755
index 0000000..67a4ba4
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diff --git a/fragpair_scoring.pyc b/fragpair_scoring.pyc
new file mode 100755
index 0000000..15fc921
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diff --git a/gui.pyc b/gui.pyc
new file mode 100755
index 0000000..e08c823
Binary files /dev/null and b/gui.pyc differ
diff --git a/mass_recal.py b/mass_recal.py
index 77db412..f690518 100755
--- a/mass_recal.py
+++ b/mass_recal.py
@@ -34,7 +34,15 @@ def run_xi_lin(peakfile, fasta, cnf, outpath, xipath, threads='1'):
 
 
 def get_ppm_error(xi_df, outfile):
-    xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > 6)] # TODO: new xi version requires lower score?
+    score_cutoff = 2
+    xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > score_cutoff)] 
+    xi_df_decoy = xi_df[(xi_df.decoy == 1) & (xi_df['match score'] > score_cutoff)]
+    
+    while (len(xi_df_decoy.index)>0.02*len(xi_df.index))
+        score_cutoff=min(xi_df['match score'][xi_df['match score'] > score_cutoff]);
+        xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > score_cutoff)] 
+        xi_df_decoy = xi_df[(xi_df.decoy == 1) & (xi_df['match score'] > score_cutoff)] 
+    
 
     median_err = np.median(xi_df['Precoursor Error'])
     try:
@@ -134,7 +142,7 @@ def main(mgf, fasta, xi_cnf, outpath, threads, xi_jar='./resources/XiSearch_1.6.
     fasta = '//130.149.167.198/rappsilbergroup/users/MitoProject/For Swantje/20170109_uniprot_mitoIDrun_FASTA.fasta'
     outpath = base_dir + '/error_shift'
     for in_file in os.listdir(mgf_dir):
-        if '.mgf' in in_file:
+        if in_file.endswith('.mgf') and not in_file.startswith('recal_') :
             main(mgf=os.path.join(mgf_dir, in_file),
                  fasta=fasta,
                  xi_cnf='D:/user/Swantje/projects/pipeline_prepro_xi_fdr/resources/xi_linear_by_tryp.conf',
diff --git a/mass_recal.pyc b/mass_recal.pyc
new file mode 100755
index 0000000..9af08c1
Binary files /dev/null and b/mass_recal.pyc differ
diff --git a/mass_recal_ms2.py b/mass_recal_ms2.py
index 0e98881..f33bfc7 100755
--- a/mass_recal_ms2.py
+++ b/mass_recal_ms2.py
@@ -35,7 +35,15 @@ def run_xi_lin(peakfile, fasta, cnf, outpath, xipath, threads='1'):
 
 
 def get_ppm_error(xi_df, peaks_df, outfile):
-    xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > 6)]
+    score_cutoff = 2
+    xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > score_cutoff)]
+    xi_df_decoy = xi_df[(xi_df.decoy == 1) & (xi_df['match score'] > score_cutoff)]
+
+    while (len(xi_df_decoy.index)>0.02*len(xi_df.index)):
+        score_cutoff=min(xi_df['match score'][xi_df['match score'] > score_cutoff]);
+        xi_df = xi_df[(xi_df.decoy == 0) & (xi_df['match score'] > score_cutoff)]
+        xi_df_decoy = xi_df[(xi_df.decoy == 1) & (xi_df['match score'] > score_cutoff)]
+    
     median_err = np.median(xi_df['Precoursor Error'])
     try:
         fig, ax = plt.subplots()
@@ -156,7 +164,7 @@ def main(mgf, fasta, xi_cnf, outpath, threads, xi_jar='./resources/XiSearch_1.6.
     fasta = '//130.149.167.198/rappsilbergroup/users/MitoProject/For Swantje/20170109_uniprot_mitoIDrun_FASTA.fasta'
     outpath = base_dir + '/error_shift'
     for in_file in os.listdir(mgf_dir):
-        if '.mgf' in in_file:
+        if in_file.endswith('.mgf') and not in_file.startswith('recal_'):
             main(mgf=os.path.join(mgf_dir, in_file),
                  fasta=fasta,
                  xi_cnf='D:/user/Swantje/projects/pipeline_prepro_xi_fdr/resources/xi_linear_by_tryp.conf',
diff --git a/preprocessing.py b/preprocessing.py
index 6ae04b3..bdf25d0 100755
--- a/preprocessing.py
+++ b/preprocessing.py
@@ -300,7 +300,7 @@ def process_file(filepath, outdir, mscon_settings, split_acq, detector_filter, m
     pool.close()
     pool.join()
 
-    recal_in = [os.path.join(outdir, x) for x in os.listdir(outdir) if '.mgf' in x]
+    recal_in = [os.path.join(outdir, x) for x in os.listdir(outdir) if x.endswith('.mgf') and not x.startswith('recal_')]
     if recal:
         # pool = Pool(processes=nthr)
         if not os.path.exists(outdir):
diff --git a/preprocessing.pyc b/preprocessing.pyc
new file mode 100755
index 0000000..daab717
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diff --git a/preprocessing_ms2recal.py b/preprocessing_ms2recal.py
index 558e25a..49c02c4 100755
--- a/preprocessing_ms2recal.py
+++ b/preprocessing_ms2recal.py
@@ -300,7 +300,7 @@ def process_file(filepath, outdir, mscon_settings, split_acq, detector_filter, m
     pool.close()
     pool.join()
 
-    recal_in = [os.path.join(outdir, x) for x in os.listdir(outdir) if '.mgf' in x]
+    recal_in = [os.path.join(outdir, x) for x in os.listdir(outdir) if  x.endswith('.mgf') and not x.startswith('recal_')]
     if recal:
         # pool = Pool(processes=nthr)
         if not os.path.exists(outdir):