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 <jwin...@gmail.com<mailto:jwin...@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-discuss+unsubscr...@googlegroups.com<mailto:spctools-discuss+unsubscr...@googlegroups.com>. To post to this group, send email to spctools-discuss@googlegroups.com<mailto: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. 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.
