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 <[email protected] <javascript:>> > 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 [email protected] <javascript:>. > To post to this group, send email to [email protected] > <javascript:>. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
