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]> 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] 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, 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]. > 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. > > -- 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.
