Closed anuC closed 1 month ago
Peptide "KARLSLEQLSHTPGSR" has two missed cleavage sites but the parameter setting only allows a maximum of one missed cleavage site.
If you really want to include that peptide, you could add this parameter "-c 2" by set the allowed maximum missed cleavage site to 2. But this will slow down the search.
Thank you the prompt reply.
Hi,
I am using standalone version of PepQuery for protein identification. After trypsin digestion, PepQuery identified below peptides as unique. However, it seems like trypsin digestion with Pepquery is incomplete, as I could note that some peptides are missed. The following command was used with PepQuery
java -Xmx30G -jar pepquery-2.0.2/pepquery-2.0.2.jar -b CPTAC -db GRCh38_latest_protein.fasta -hc -s 1 -m 1 -o pepquery_out/ -i MIKFSWSQTMRTEWRKARLSLEQLSHTPGSRTPRLFCS -t protein -fast
PepQuery listed following peptides as unique
However,I could see that a peptide with sequence - KARLSLEQLSHTPGSR, is missing in the above list. As the peptide ARLSLEQLSHTPGSR is listed as the unique peptide, I wonder why PepQuery missed a very similar peptide KARLSLEQLSHTPGSR being listed as the unique one?