Thanks very much for your answers - that's very helpful! Alastair Am Freitag, 13. Dezember 2019 21:56:04 UTC+1 schrieb Eric Deutsch: > > Thanks for the clarification, Jimmy! > > > > *From:* [email protected] <javascript:> < > [email protected] <javascript:>> *On Behalf Of *Jimmy Eng > *Sent:* Friday, December 13, 2019 8:27 AM > *To:* [email protected] <javascript:> > *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] <javascript:>> 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] <javascript:>. > 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] <javascript:>. > 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> > . >
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