Hi,
Can someone explain what's happen here please:
Number of spectra in the .mgf file = 1856
Number of spectra after conversion to mzXML = 1856
Number of spectra in pepXML file after comet search: 1752
I then search against database A (DB-A) and database B (DB-B) and count the
number of spectra in the pepXML file as counts of "<spectrum_query
spectrum=". Yields 1752 in both cases.
I then run "xinteract -Neg.pepXML -PPM -dDECOY_ -OARP eg_pepp.pepXML" on
each of the files. Now when I search for the string "<spectrum_query
spectrum=" I get 481 hits for DB-A and 632 hits for DB-B. The pepXML view
then calculates the "Efficiency ID'd/searched" - so the denominator is
different for each database.
Can someone help to explain this behavior?
- Why does the xinteract output present different numbers of records
("<spectrum_query spectrum= ...") for the two different databases, even
though the number of records in the pepXML input was the same?
- Isn't the definition of 'Spectra searched' used by Petunia misleading?
It's not the number of input spectra to the search engine.
- Presumably the loss of spectra between the input to comet and the
output is due to loosing those spectra with absolutely no match to the
database or decoys due to some internal threshold on the score for PSMs.
Any help would be hugely appreciated!
Thanks,
Alastair
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