Hi Alistair, thanks for posting your questions. Although it’s possible something problematic is happening, I think the answers to your questions are:
1) Most search engines including Comet have a minimum spectrum quality threshold to even search the spectrum, e.g. minimum of 10 peaks. There are settings in the comet.params. Also, if your database is very small (not generally recommended) with very narrow tolerances, there may not be any possible peptides that match the query spectrum precursor m/z within tolerance. In both cases, there is no result from the search engine, and therefore nothing in the pepXML 2) My best guess here is: the default behavior of PeptideProphet is to NOT write out any spectra with probability < 0.05 to the output file so that it is smaller and faster to explore. You can turn off this behavior with the -p0 option to xinteract. This will pass through all PSMs. *From:* 'Alastair Skeffington' via spctools-discuss < [email protected]> *Sent:* Friday, December 13, 2019 2:29 AM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] Interpretation of stats from pepXML viewer 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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/09b3c5de-a9b9-46be-8b40-d502a5c17bf6%40googlegroups.com <https://groups.google.com/d/msgid/spctools-discuss/09b3c5de-a9b9-46be-8b40-d502a5c17bf6%40googlegroups.com?utm_medium=email&utm_source=footer> . -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/eb531ba4ec1aeb9c64423555be94a501%40mail.gmail.com.
