my %seen;  # a new global variable
...
   # then, whenever you 'createElement' and/or 'setAttribute', first assemble the string:
   #my $materialmapping_item2 = $materialmapping_table_xml->createElement("item3");
   #$materialmapping_item2->setAttribute(decode('cp1252',$pr_cell_name2->{Val}),$pr2);
   my $entry = join',', decode('cp1252',$pr_cell_name2->{Val}),$pr2;

   # and create it if it doesn't already exist:
   if (!exists $seen{$entry}++){
      my $materialmapping_item2 = $materialmapping_table_xml->createElement("item3");
      $materialmapping_item2->setAttribute($entry);
   }