As a remark to Erics second point, this paper is enlightening: The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis Giselle M. Knudsen, Robert J. Chalkley http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020873
Hannes On 4 April 2014 16:31, Eric Deutsch <[email protected]> wrote: > I would just like to second what Hannes says: when using PeptideProphet, > never suppress the output of any negative results from the search engine > (X!Tandem or others) no matter how bad. PeptideProphet uses all this > information to model and discriminate between the correct and incorrect > identification distributions. > > While I'm on the soap box, I'd like to mention another "don't": never > suppress from your sequence fasta file any sequences that you know or > strongly suspect are in your sample. If you know you have E coli > contamination that you don't care about, do not leave out the E coli > sequences. Do include all the discoverable sequences, let the search engine > find them, let the prophets model them, and then discard those IDs if you > don't care about them. > > Eric > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Hannes Röst > Sent: Friday, April 04, 2014 1:27 AM > To: [email protected] > Subject: Re: [spctools-discuss] Can PeptideProphet and iProphet succeed > with > few matched decoys? > > Dear Vadim > > I just checked my xtandem ini files and we have used these parameters > > <note type="input" label="output, results">all</note>^M > <note>values = all|valid|stochastic</note>^M > <note type="input" label="output, maximum valid expectation > value">0.1</note>^M > <note>value is used in the valid|stochastic setting of output, > results</note>^M > > according to the documentation, this will write out all results without any > E value filtering. As far as I understand the PeptideProphet algorithm, it > is necessary to report all results if you want to use PeptideProphet and > very likely the modelling will not work as expected when you perform any E > value filtering. I would thus suggest to also set the output, results value > to "all". I have attached the xml files that I currently use for your > convenience. > > If you are interested in how we created the spectral libraries for the > OpenSWATH paper, please consult the method section available in the online > supplementary. There we describe our searches and how we converted the > X!Tandem searches to SpectraST and then TraML files. > > I hope that helps > > Hannes > > > On 4 April 2014 01:24, Vadim Patsalo <[email protected]> wrote: > > Dear Hannes, thank you for your reply. > > > > By "filter," I assume you mean the "maximum valid expectation value" in > > the output and refine settings of X!Tandem? > > If so, I've performed the following experiment. > > > > Evalue 1e-2: 8 decoys / 24280 non-decoys > > Evalue 1e-1: 105 decoys / 31902 non-decoys > > Evalue 1e0: 793 decoys / 38363 non-decoys > > Evalue 1e1: 3197 decoys / 42706 non-decoys Evalue 1e2: 4642 decoys / > > 44256 non-decoys > > > > Thank you for your advice -- I will attempt to build the Pos and Neg > > distributions using the more liberal cutoffs. > > My goal is to obtain a SpectraST library to interrogate SWATH datasets, > > using OpenSWATH, of course! > > > > What kind of decoy to non-decoy ratio is satisfactory for FDR modelling, > > in your experience? > > > > Vadim > > > > On Apr 3, 2014, at 11:28 AM, Hannes Röst <[email protected]> wrote: > > > >> Hi Vadim > >> > >> This will most likely _not_ work. It would probably be better if you > >> do not filter before xinteract but give it the full X!Tandem output > >> and then filter afterwards based on the computed probabilities. This > >> way you also might increase the total number of retained hits at a > >> fixed FDR. > >> > >> Hannes > > > > -- > > 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 post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/spctools-discuss. > > For more options, visit https://groups.google.com/d/optout. > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
