Hi Dave, Thanks for following up. I had tried to use the CPFP demo server for a test with some of our data. Unfortunately I never made it past the search steps in the workflow. I just logged in and the two samples I'm trying to compare still report the status "SEARCHES QUEUED/RUNNING" and so I have not yet been able to attempt SINQ normalization.
If you let me know when things get sorted on your end, I'd love to try SINQ normalization as a comparison with our other approaches. Thanks! Greg On Monday, April 1, 2013 2:27:27 PM UTC-7, Dave Trudgian wrote: > > Hi Greg, > > Just a quick note that if you happen to have tried SINQ on CPFP and have > had any problems with the demo server I apologize. I had been away for a > while and not really monitoring it, so may not have worked for you. Am > going to spend some time on CPFP soon. > > If you happen to try it on CPFP and have any problems then let me know. > > DT > > On Monday, March 18, 2013 1:23:48 PM UTC-5, Greg Cary wrote: >> >> 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]> 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]. >>> > 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. 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