Greg, Sorry about that - I'll have it fixed tomorrow and contact you off list. The CPFP daemons are/were quite flaky, hence they break if any of various dependencies have any issue / the OS decides to upgrade and restart them etc. Am working on this, with help from others.
Will get back to you off list as this isn't a TPP matter itself. DT On Monday, April 1, 2013 4:46:45 PM UTC-5, Greg Cary wrote: > > 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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