Micheleen, That would be great! Let me know if you get approval.
As I recall, the Normalized Spectral Index calculation (as outlined in the Nature Biotech paper) depends on Sequest-searched data (i.e. the DTAselect-filter.txt). Does your python script make the same requirement? Or does it extract the MS2 intensities from other files? I guess I can always re-search my data with Sequest... Thanks so much! Greg On Friday, March 15, 2013 1:52:01 PM UTC-7, [email protected] wrote: > > 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.
