Dear, If non-specific cleavage is selected in pFind, the choice of enzyme species 
will only bring about a small difference in the results. Considering your needs, we 
recommend choosing noenzyme and setting up non-specific cleavage.

thank you, I notice that when I choosed different enzyme types such as trypsin 
and formic acid D_C in different non-specific searches with the other parameters 
unchanged, I got two different results finally. That means the enzyme type could 
affect the final result even in the non-specific type. 
When I search endogenous peptides in Mascot or Peaks, the "none" enzyme type is 
suggested in manual. 
Is there perferred enzyme type in pFind when I search endogenous peptides ?

Dear, endogenous peptides are not usually produced by protein digestion, but are 
naturally present in the body I think. Therefore, they may not meet the rules of 
enzyme digestion and need to be searched by non-specific.

Thank you!
And there is a another question, when I choose the "Non-specific" parameter, is  
there any limitation of the enzyme type in endogeous peptides search? Or dose it 
mean that any enzyme I could choose will be OK?

Dear, When searching for endogeous peptides, please select the Non-Specific 
parameter, or check the open search option. Both options are marked in the attached 
image.

hi, I have some questions about endogeous peptides search. 
When I search the endogenous peptides, how should I set the enzyme selection in 
pFind. 
And is there any other notice when I search the endogeous peptides by pFind?