Hi all I am trying to use the latest version TPP (4.3.1) to run some cICAT data I collected a while ago. All these cICAT data have been searched by Mascot. I also have run the tutorial data (raft with older version of ICAT labeling) on my computer. Since the tutorial data were searched by Sequest, so I looked up spctools-discuss for some discussion about Mascot data, but I still have some Mascot related questions. I am currently using Mascot server 2.2.04.
1. If I have a Mascot.dat file, then can I directly start with “Analysis Pipeline (Mascot)/ pepXML” (don’t need any database search under TPP) ? In “pepXML/ 2. Specifiy Database Used in Mascot Search” means that I need to put the EXACT database I used for this searche? For instance, my searches were done by against database SwissProt 55.6, so do I need to choose the SwissProt_55.6.fasta file here? The current SwissPort version is 57.12 in our lab, can I use SwissProt_57.12.fasta file for this step? If not, where can I download the older version SwissProt database? I tried, sounds silly, but I didn’t find any archive for downloading the older SwissProt database .fasta files. Anyway, I searched my data again under current SwissProt database (57.12), but still didn’t get it worked. Here is the error massage I got (more details see attachment). c:/Inetpub/wwwroot/ISB/data/SSM4-1/F030337.pep.xml [ Unreadable! ] command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/ SSM4-1/F030337.dat -Dc:/Inetpub/wwwroot/ISB/data/SwissProt_57.12.fasta -Etrypsin" failed: Operation not permitted Command FAILED 2. I also tried to use Mascot.xml and .pepxml files to directly start with “Analyze Peptide”. The .xml gave no result (can’t open the pepXML Viewer) and I couldn’t convert it into pepXML format under pepXML in TPP. If I used .pepxml file from Mascot, it gave the results but not including any XPRESS and ASAPRatio result. From the online discussion, it seems the Mascot.dat files work better than xml/pepxml files in TPP. If I can get 1st problem resolved, then I don’t need to worry about this 2nd problem. Detailed error messages please see attachment. Many thanks for any assistance! Fay -- 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.
