diff --git a/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java b/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
index b16f9f6..5c66bf3 100644
--- a/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
+++ b/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
@@ -550,7 +550,7 @@ public static void main(String [] args) throws Exception {
 					Double.parseDouble(params.get("precursor_tol")),
 					Integer.parseInt(params.get("precursor_mass_units")),
 					datasets, mzMap, Integer.parseInt(params.get("threads")),
-					params.get("localization_allowed_res"), Float.parseFloat(params.get("spectra_tol")),
+					params.get("localization_allowed_res"), Float.parseFloat(params.get("spectra_ppmtol")),
 					concatIonTypes(), Double.parseDouble(params.get("iterloc_convergeCriterion")),
 					Integer.parseInt(params.get("iterloc_maxEpoch"))
 			);