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bzhanglab / PepQuery

PepQuery: a targeted peptide search engine
http://pepquery.org
GNU General Public License v3.0
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Trypsin digestion and unique peptide identification #69

Closed anuC closed 1 month ago

anuC commented 2 months ago

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

^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.PepMapping[init:88] - Indexing took 0.483184339 seconds and consumes 246.462 MB ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - FSWSQTMR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - MIKFSWSQTMR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - FSWSQTMRTEWR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - LSLEQLSHTPGSR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - ARLSLEQLSHTPGSR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - LSLEQLSHTPGSRTPR is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.InputProcessor[run:178] - TPRLFCS is not exist in the reference protein database. ^[[m^[[32m2024-08-07 10:59:25 [INFO ] main.java.pg.PeptideSearchMT[search:395] - Total target peptides:7, unique peptides:7, shared peptides:0

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?

wenbostar commented 2 months ago

Peptide "KARLSLEQLSHTPGSR" has two missed cleavage sites but the parameter setting only allows a maximum of one missed cleavage site.

wenbostar commented 2 months ago

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.

anuC commented 1 month ago

Thank you the prompt reply.