Great Micheleen! I have all of the requisite data you mention as I have processed and analyzed my data using standard TPP protocols.
I'm looking forward to testing out this normalization on our data. Greg On Friday, March 15, 2013 2:20:22 PM UTC-7, Micheleen Harris wrote: > > Hi Greg, > > You may search with any engine you wish (I've tested with X!Tandem, > Myrimatch, Comet, which is based on Sequest, and OMSSA). The NSI > application I've written needs the following(there are also a few > other parameters for input and output such as the directory of the > input files): > > 1) either mzML or mzXML files > 2) an IProphet pep.xml (combining all your individual pep.xml files > from the search(s)) - The IProphet tool is available with the TPP. > 3) the fasta file you used for the search > 4) An FDR cutoff for the pep.xml file > > Go ahead and do a search and run IProphet on the pep.xml files. I'll > let you know when the code is available. > > Best, > Micheleen > > On Fri, Mar 15, 2013 at 2:02 PM, Greg Cary <[email protected]<javascript:>> > wrote: > > 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]: > >> > >> 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, SIn,NSI/NSMT). 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 a topic in the > > Google Groups "spctools-discuss" group. > > To unsubscribe from this topic, visit > > > https://groups.google.com/d/topic/spctools-discuss/KbPZ6Ad4XLs/unsubscribe?hl=en. > > > > To unsubscribe from this group and all its topics, send an email to > > [email protected] <javascript:>. > > To post to this group, send email to > > [email protected]<javascript:>. > > > Visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- 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.
