just curiois! have u tried XPRESS?? On large datasets, in our lab, ASAP gave us a lot of problems while XPRESS worked.
On Wed, Nov 21, 2012 at 4:41 PM, Alex <[email protected]> wrote: > Thanks Brain for your quick reply, > > I'm running a dimethylation experiment (Ligth+28, Heavy+32). Until now, I > have been acquiring data with a QTRAP2000, and everything worked nicely > using the static approach (but not much proteome coverage with this MS). We > now got a VelosPRO Orbitrap, and I am reacquiring the same samples!!!. I'm > running X!Tandem, and DB search worked so far for protein ID. When I > ANALYZE peptides with ASAPratio, things crash after 2-3 hours with this > message. Until now, I have always been using the STATIC approach (according > to the many threads I have reviewed on this topic), where I repeat the DB > search for the light and heavy using two different parameters search. It > used to work fine with the QTRAP2000 data. Of course, my files with the > orbitrap are much larger, so I was suspecting I was running into some > memory issue (Im not sure what this Runtime is all about). > > I'll try with your approach, if you have any other ideas, welcome!!! > > Alex > > > On Wednesday, 21 November 2012 10:40:06 UTC-4, Brian Hampton wrote: > >> I've never gotten the static option to work. I'm not sure how the static >> option is intended to be used..... correctly e.g. What type of data set. >> >> If you are doing two searches one with the static light and the second >> with the static heavy isotope labels, you will have to redo the search and >> do it as per the Tandem API where you set the light to be a static mod and >> the mass difference between the heavy and light to be a variable mod. In >> addition to giving results ASAPRatio can quantitate, it has been noted that >> the second search method is more statistically sound because it increases >> the size of the database as a result of the variable mods. >> >> Using the second search strategy has reduced ASAPRatio processing time on >> my data sets from many hours to about a half hour. Also, using the static >> option on Linux w/ TPP 4.5.2 ASAPRatio would complete after hours. But I >> have problems with the viewers not working in Linux so after switching to >> Win for the quan analysis, using TPP 4.6.1 the static option always kicks >> out an error and quits. Feeding it search results as mentioned above it >> all works and completes much more quickly. >> >> Why the static option doesn't work on our data sets is a mystery to me. >> >> Brian >> >> >> On Nov 21, 2012, at 8:33 AM, Alex <[email protected]> wrote: >> >> I think my post didn't show up correctly. Here it goes again! >> >> Hi TTP community, >> >> I'm running some ASAPratio quant on a 2D-LC-MSMS experiment on windows XP >> running TPP v4.5 RAPTURE rev 2, Build 201202031108 (MinGW). After a >> couple of hours analysis I get the following error. Has somebody run >> into this problem before??? Any ideas much appreciated!!! >> >> >> Alex >> >> >> Error Message: >> >> This application has requested the Runtime to terminate it in an unusual >> way. >> Please contact the application's support team for more information. >> command "C:/Inetpub/tpp-bin/**ASAPRatioPeptideParser "interact.pep.xml" >> -lKn -F -C -r0.1 -S -mK160.15137n33.06425" failed: No such process >> command "C:/Inetpub/tpp-bin/**ASAPRatioPeptideParser "interact.pep.xml" >> -lKn -F -C -r0.1 -S -mK160.15137n33.06425" exited with non-zero exit code: 3 >> QUIT - the job is incomplete >> command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -Op >> -I1 -I4 -I5 -A-lKn-F-C-r0.1-S-mK160.**15137n33.06425 >> 2DYeast01.tandem.pep.xml >> 2DYeast02.tandem.pep.xml 2DYeast03.tandem.pep.xml >> 2DYeast04.tandem.pep.xml 2DYeast05.tandem.pep.xml 2DYeast06.tandem.pep.xml >> 2DYeast07.tandem.pep.xml 2DYeast08.tandem.pep.xml >> 2DYeast09.tandem.pep.xml 2DYeast10.tandem.pep.xml 2DYeast11.tandem.pep.xml >> 2DYeast12.tandem.pep.xml 2DYeast13.tandem.pep.xml >> 2DYeast14.tandem.pep.xml 2DYeast15.tandem.pep.xml 2DYeast16.tandem.pep.xml >> 2DYeast17.tandem.pep.xml 2DYeast18.tandem.pep.xml >> 2DYeast19.tandem.pep.xml 2DYeast20.tandem.pep.xml 2DYeast21.tandem.pep.xml >> 2DYeast22.tandem.pep.xml 2DYeast23.tandem.pep.xml >> H2DYeast01.tandem.pep.xml H2DYeast02.tandem.pep.xml >> H2DYeast03.tandem.pep.xml >> H2DYeast04.tandem.pep.xml H2DYeast05.tandem.pep.xml >> H2DYeast06.tandem.pep.xml H2DYeast07.tandem.pep.xml >> H2DYeast08.tandem.pep.xml >> H2DYeast09.tandem.pep.xml H2DYeast10.tandem.pep.xml >> H2DYeast11.tandem.pep.xml H2DYeast12.tandem.pep.xml >> H2DYeast13.tandem.pep.xml >> H2DYeast14.tandem.pep.xml H2DYeast15.tandem.pep.xml >> H2DYeast16.tandem.pep.xml H2DYeast17.tandem.pep.xml >> H2DYeast18.tandem.pep.xml >> H2DYeast19.tandem.pep.xml H2DYeast20.tandem.pep.xml >> H2DYeast21.tandem.pep.xml H2DYeast22.tandem.pep.xml >> H2DYeast23.tandem.pep.xml" failed: No >> such process >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To view this discussion on the web visit https://groups.google.com/d/** >> msg/spctools-discuss/-/**K9ou37m9EhEJ<https://groups.google.com/d/msg/spctools-discuss/-/K9ou37m9EhEJ> >> . >> To post to this group, send email to spctools...@googlegroups.**com. >> To unsubscribe from this group, send email to spctools-discu...@** >> googlegroups.com. >> >> For more options, visit this group at http://groups.google.com/** >> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >> . >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/1HV_Ukku1HAJ. > > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- Kshitiz Tyagi -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
