Our Endoproteinase Asp N works better on peptide substrates than on intact proteins, so we suggest either using another enzyme to first generate large peptides that Endoproteinase AspN will have less trouble digesting (a double digest with either Trypsin or Endoproteinase GluC) or switching to another source of Endoproteinase AspN as our Endoproteinase AspN enzyme is different from other commercial sources.