CometAdapter: Meaning of "Omitted writing of XXX peptide identifications due to empty hits." #6456

polklin · 2022-11-09T09:47:22Z

polklin
Nov 9, 2022

Hello,

I was wondering what is the meaning of the message "Omitted writing of 636 peptide identifications due to empty hits." at the end of my CometAdapter command ? (see last line of the screenshot below)
Is that something I should worry about ? I am very new to mass spec so sorry if that is a trivial question !

Using prefix decoy string 'DECOY_'
Info: using 'unspecific cleavage' as enzyme (obtained from idXML) for digestion.
Peptide identification engine: COMET
Enzyme: unspecific cleavage
Info: using 'full' as enzyme specificity (obtained from idXML) for digestion.

 Progress of 'Load first DB chunk':

 -- done [took 0.22 s (CPU), 0.22 s (Wall)] -- 
Building trie ... done (0s)
Compressing trie to BFS format ...
done (0s)
Mapping 18810 peptides to 94466 proteins.
Searching with up to 3 ambiguous amino acid(s) and 0 mismatch(es)!

 Progress of 'Aho-Corasick':

 -- done [took 4.62 s (CPU), 0.52 s (Wall)] -- 
Merge took: 0.01 s (wall), 0.02 s (CPU), 0.00 s (system), 0.02 s (user)
Memory usage (Aho-Corasick): 38 MB (working set delta), 38 MB (peak working set delta)


Aho-Corasick done:
 found 46127 hits for 18810 of 18810 peptides.
Peptide hits passing enzyme filter: 46127
    ... rejected by enzyme filter: 0
-----------------------------------
Peptide statistics

 unmatched                : 0 (0 %)
 target/decoy:
   match to target DB only: 11673 (62 %)
   match to decoy DB only : 7062 (37 %)
   match to both          : 75 (0 %)

 mapping to proteins:
   no match (to 0 protein)         : 0
   unique match (to 1 protein)     : 8562
   non-unique match (to >1 protein): 10248
-----------------------------------
Protein statistics

 total proteins searched: 94466
 matched proteins       : 25099 (25099 new)
 matched target proteins: 14198 (56 %)
 matched decoy proteins : 10901 (43 %)
 orphaned proteins      : 132 (all removed)
-----------------------------------
Omitted writing of 636 peptide identifications due to empty hits.
CometAdapter took 04:17 m (wall), 7.26 s (CPU), 0.36 s (system), 6.90 s (user); Peak Memory Usage: 177 MB.

Best,
Paul

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CometAdapter: Meaning of "Omitted writing of XXX peptide identifications due to empty hits." #6456

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CometAdapter: Meaning of "Omitted writing of XXX peptide identifications due to empty hits." #6456

polklin Nov 9, 2022

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polklin
Nov 9, 2022