Ian, The quick test is to repeat the search using your older files with the newer TPP install. Use the same search parameters as you did before. If you get your 300+ identifications then the problem is likely with your new data files. If you don't get the expected number of IDs as you got before (on the same data using the same parameters) then maybe you did discover a bug.
On Fri, Sep 25, 2009 at 11:50 AM, Ian <[email protected]> wrote: > > Hi all, > I was getting this same error, so I upgraded to the newer TPP and it > works, but the searches do not seem to be producing very good results. > I'm only getting 0-40 identified peptides with expectation scores < > 0.1, where I would have expected 300+ on similar older files. How can > I determine if it is my data files, search parameters, or a bug? > > Ian > > On Sep 9, 2:04 pm, Oded <[email protected]> wrote: >> Thanks Natalie, >> >> On Sep 9, 11:57 pm, Natalie Tasman <[email protected]> >> wrote: >> >> > Hello Oded, >> >> > Please see the recently released 4.3.1 version of the TPP, which >> > contains the fix that you mention. >> >> > Best wishes, >> >> > Natalie >> >> > On Sep 9, 2009, at 12:49 PM, Oded wrote: >> >> > > Hi , >> > > Is it possible to get this bug fix (thanks again Brian) into windows >> > > installation package? >> > > Thanks, >> > > Oded >> >> > > On Aug 17, 9:48 pm, "Brian Pratt" <[email protected]> wrote: >> > >> It would be interesting to see the difference between themzXMLfile >> > >> that >> > >> worked and the one that didn't. >> >> > >>X!Tandemhas its ownmzXMLparser and it might need a tweak. Perhaps >> > >> you >> > >> could send me those files? >> >> > >> Thanks, >> >> > >> Brian >> >> > >> -----Original Message----- >> > >> From: [email protected] >> >> > >> [mailto:[email protected]] On Behalf OfOded >> > >> Sent: Saturday, August 15, 2009 1:08 PM >> > >> To: spctools-discuss >> > >> Subject: [spctools-discuss] RAW tomzXML(and mzXL) problem TPP4.3 >> >> > >> Hi, >> > >> I'm having problems converting RAW data tomzXMLwith TPP4.3. >> > >> I tested different files on 2 different WinXP computers installed >> > >> with >> > >> TPP4.3. The conversion tomzXMLgoes just fine and the output can be >> > >> used with Pep3D. >> > >> However, while trying to run aTandemsearch with the TPP4.3- >> > >> generatedmzXMLfile as input the followingerrormessage pop-up: >> > >> run_in.exeerror >> > >> run_in.exe has encountered a problem and needs to close. We are >> > >> sorry >> > >> for the inconvenience. >> > >> In the detailes section I can see that theerrorsignature is: >> > >> szAppName : run_in.exe szAppVer : 0.0.0.0 szModName : >> > >> msvcrt.dll >> > >> szModVer : 7.0.2600.5512 offset : 00037b26 >> > >> If I try to use the samemzXMLforX!Tandemsearch on a Mac running >> > >> TPP 4.3 (or 4.2) I'm getting the following message: >> > >>X!TANDEM2 (2007.07.01.3) >> > >> Loading spectra .Unsupportedcompressiontype 'none'. >> > >> Command FAILED >> > >> I tried to use different conversion options (i.e profile, centroid, >> > >> with or with out comprssing) but still got the sameerrormessages. >> >> > >> In addition conversion to mzXL failed showing the followingerror >> > >> message >> >> > >> c:\Inetpub\tpp-bin\msconvert -v --mzML -o c:/Inetpub/wwwroot/ISB/ >> > >> data/ >> > >> Test/Markers -c [1,2] c:/Inetpub/wwwroot/ISB/data/Test/Markers/ >> > >> LFok08.RAW >> >> > >> Unable to read configuration file [1,2] >> >> > >> format: mzML (Precision_64 [ 1000514:Precision_64 >> > >> 1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None) >> > >> indexed="true" >> > >> outputPath: c:/Inetpub/wwwroot/ISB/data/Test/Markers >> > >> extension: .mzML >> > >> contactFilename: >> >> > >> filters: >> >> > >> filenames: >> > >> c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW >> >> > >> processing file: c:/Inetpub/wwwroot/ISB/data/Test/Markers/LFok08.RAW >> > >> [MSDataFile::readFile()] Unsupported file format. >> > >>Errorprocessing file c:/Inetpub/wwwroot/ISB/data/Test/Markers/ >> > >> LFok08.RAW >> >> > >> Converting the same files on TPP4.2 (rev1) generate fully >> > >> "fuctional"mzXMLfiles. >> > >> Any help would be appreciated,Oded > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
