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 Inviato: giovedì 14 dicembre 2017 21:15 A: [email protected] 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: [email protected] [mailto:[email protected]] 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 <[email protected]> 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]. 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. -- 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. -- 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 [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. -- 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.
