diff --git a/modules/local/openms/isobaricanalyzer/main.nf b/modules/local/openms/isobaricanalyzer/main.nf
index c4c7596d..b15cedc2 100644
--- a/modules/local/openms/isobaricanalyzer/main.nf
+++ b/modules/local/openms/isobaricanalyzer/main.nf
@@ -35,15 +35,19 @@ process ISOBARICANALYZER {
         }
 
         // Read the matrix file and format it into the command-line format
+        // Read the matrix file, skipping lines that start with '#' and process the matrix
         def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
         .findAll { !it.startsWith('#') && it.trim() } // Skip lines starting with '#' and empty lines
         .drop(1) // Assuming the first non-comment line is a header
         .collect { line ->
             def values = line.split('/')
-            return "${values[1]}/${values[2]}/${values[3]}/${values[4]}"
+            return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
         }
-        def correction_matrix = matrix_lines.join(", ")
-        isotope_correction += " -${meta.labelling_type}:correction_matrix \"${correction_matrix}\""
+
+    // Join the matrix lines into a format for the C++ tool
+    def correction_matrix = matrix_lines.join(", ")
+
+    isotope_correction += " -${meta.labelling_type}:correction_matrix ${correction_matrix}"
     }
 
     """