Hi Greg, We have implemented the Normalized Spectral Index (SIn) as a python script at ISB. It is not available on regis yet as a production command line application, but the plan is to offer it in the future. If you would like the code I could send it to you via DropBox as long as I get approval to do so. Would you be interested in this?
Best, Micheleen Harris On Thursday, March 14, 2013 11:38:33 AM UTC-7, Greg Cary wrote: > > Hi all, > > I've been reading a lot lately about a variety of label-free quantitation > techniques. Unfortunately our data is poorly suited to MS1 peak > extraction/integration (a la maxquant, skyline MS1 filtering etc.) and so > we're very keen to implement some form of spectral counting (MS2 level) to > compare complex co-purification from two different conditions. It seems > that in the world of spectral counting, recent movements have been toward > some form of normalization that depends on extracting information from MS2 > fragment ion intensities (e.g. > SINQ<http://www.ncbi.nlm.nih.gov/pubmed/21656681> > , SIn > <http://www.ncbi.nlm.nih.gov/pubmed/20010810>,NSI/NSMT<http://www.ncbi.nlm.nih.gov/pubmed/22582177>). > > It appears that the CPFP at UT Southwestern has included SINQ quantitation > as part of their dist via a perl module. I'm wondering whether there are > any tools/scripts available on regis that would allow for the extraction of > MS2 fragment ion intensity values or if this was in > consideration/development at all? > > Thanks for any thoughts and comments on this approach! > > Greg C. > > -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
