no, have not tried Xpress. I preferred the way to visualize and analyze data on ASAP, and preferred it.... while it worked! thanks for the comment anyway
On Wednesday, 21 November 2012 12:45:01 UTC-4, kshitiz wrote: > > 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] <javascript:>>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]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/OhfR-F4z1dMJ. 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.
