This may mean testing several orders of magnitude more peptides than if trypsin cleavage had been specified. Otherwise, ignoring the enzyme specificity increases the number of random matches which will reduce scoring discrimination. If the search fails to produce a positive match, then try again with no enzyme specificity. Monoisotopic or Average Specify whether the experimental mass values are average or monoisotopic. If you are unsure which to choose, refer to the mass accuracy help page.
Modifications Select any known or suspected modifications .
If you are using Internet Explorer 3.x, you may find that one modification is selected by default when the form loads. This is a bug in IE3. To clear an item, hold down the control key while clicking on the selected item. Mascot supports two types of modification. Variable modifications are those which may or may not be present.