The negative values tend to throw folks off. The greater the value, the greater the abundance (e. g. -10 > -12). I find it helps to scale all the values by the minimum, shifting them all to positive when presenting the results to others.
On Dec 15, 2017 9:38 AM, "Filippo GENOVESE" <fgenov...@unimore.it> wrote: > Thanks guys. > > Could you please briefly comment on how to interpret the StPeter Sin > value? The lower, the more abundant or the other way around? > > > > Have a nice day > > > > Filippo > > > > *Da: *Michael Hoopmann <michael.hoopm...@systemsbiology.org> > *Inviato: *giovedì 14 dicembre 2017 21:15 > *A: *spctools-discuss@googlegroups.com > *Oggetto: *RE: [spctools-discuss] Re: StPeter documentation > > > > Manuscript is in review, but documentation is already under construction: > http://tools.proteomecenter.org/wiki/index.php?title=Software:StPeter > > Cheers, > > Mike > > > > *From:* spctools-discuss@googlegroups.com [mailto:spctools-discuss@ > googlegroups.com] *On Behalf Of *Filippo GENOVESE > *Sent:* Monday, December 11, 2017 4:51 AM > *To:* spctools-discuss > *Subject:* Re: [spctools-discuss] Re: StPeter documentation > > > > Any news? > > > > Filippo > > Il giorno venerdì 14 luglio 2017 01:39:01 UTC+2, Hampton, Brian ha scritto: > > Thanks Jason! Once your manuscript is published it would be great to > announce that on this list. > > > > Cheers! > > > > Brian > > > On Jul 12, 2017, at 8:13 AM, Jason Winget <jwi...@gmail.com> wrote: > > Hi Brian, > > StPeter is a direct implementation of the Normalized Spectral Index, > described by Griffin et. al: https://www.ncbi.nlm.nih. > gov/pmc/articles/PMC2805705/ > > It uses MS2 intensities for protein-level quantification. > > > > We are working on publishing it independently but so far journal editors > have not been very receptive... > > > > As for usage, if you run StPeter from the command line with no arguments > you will see a usage statement. By default it uses only non-degenerate > peptides and a 1% FDR cutoff. Typically the default values are fine, so you > should just be able to run it against your ProtXML results. It will write > the quantification values back into the ProtXML and will also output some > simple CSV results. > > > > At the moment PTMs are hard-coded and contain only a limited set, so the > most common issue that I run into is that the program will crash when > searching "unusual" mods. > > > > -Jason > > > On Friday, June 16, 2017 at 5:33:59 PM UTC-4, Brian Hampton wrote: > > Hello, > > I would be appreciative if someone could point me to documentation that > describes StPeter which is used for label-free quantification in TPP. I've > tried the usual searching with Google, PubMed and looking through the SPC > Tools sites without success. > > Thanks, > > Brian > > -- > 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 spctools-discu...@googlegroups.com. > To post to this group, send email to spctool...@googlegroups.com. > Visit this group at https://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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/-36bVjElNMo/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/-36bVjElNMo/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://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. 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