Thanks for the clarification, Jimmy!
*From:* [email protected] <[email protected]> *On Behalf Of *Jimmy Eng *Sent:* Friday, December 13, 2019 8:27 AM *To:* [email protected] *Subject:* Re: [spctools-discuss] Interpretation of stats from pepXML viewer Regarding inputs and output counts to Comet, as Eric mentioned, there are search parameters which affect whether or not a spectrum will be searched at all. These are: activation_method, digest_mass_range, max_precursor_charge, minimum_peaks, minimum_intensity, and remove_precursor_peak (which can affect minimum_peaks). A query spectrum that happens to be out of bounds for any of these parameters will not be analyzed (is effectively ignored) and will not show up in the output. Any spectra that passes these filters will have an output entry in Comet's pepXML output file, even if there's no matching peptide output. Such blank outputs can happen in cases where the database or tolerances are so small that no peptides are scored or the spectrum is so poor that the xcorr score is less than or equal to zero. This is why you see 1752 spectra in the pepXML after Comet searches of both your databases as that's the number of spectra that actually get analyzed and is a function of the input and not the database being searched. On Fri, Dec 13, 2019 at 2:29 AM 'Alastair Skeffington' via spctools-discuss <[email protected]> wrote: 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/CAJqD6EMd7QCryMAx401SY7rRNkX-MBCtAskTUtz0Kj63Bpji%2BA%40mail.gmail.com <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EMd7QCryMAx401SY7rRNkX-MBCtAskTUtz0Kj63Bpji%2BA%40mail.gmail.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/6607a03230b3a49a6e7288f39a581d36%40mail.gmail.com.
