Hello Hoikeun, Are there any errors or other messages when you convert the .sqt files to .pep.xml ? Are all files in the same directory along with the .mzML files?
As for the Mascot files, make sure you follow the following process to make sure that the .dat files are compatible with TPP: 1. .raw file to mzML (or mzXML) ==> myRun.mzML 2. Convert this file to mgf (using MzXML2Search) ==> myRun.mgf 3. Use this file as an input to MASCOT; MASCOT then generates .dat file ==> F0123456.dat 4. Rename this to the original base name ==> myRun.dat 5. Convert to pepXML ==> myRun.pep.xml 6. Analyze with PeptideProphet, etc. Cheers, --Luis On Mon, Feb 23, 2015 at 11:06 PM, Hoikeun Jeong <[email protected]> wrote: > Thanks Luis > > But I have another problems ; > > In sqt things, I got pepxml files with your suggestion and apply pepxml > files to 'analyze peptides'. > > But the results show 'Command failed' Return code : 256 > > In command windows, all result shows repetedly > file 1: ~name.pep.xml > Unknown file type. No file loaded. > WARNING: cannot open data file ~path. unknown in msms_run_summary tag... > Unknown file type. No file loaded. > WARNING: cannot CORRECT data file ~path. unknown in msms_run_summary tag... > > > Also, in mascot ~.dat paptide analyze things repeatedly show ; > > Warning: could not find scan numbers of spectrum File: name.mzXML > Scans:1507 RT:15.8351min Charge:2 Fragmentation:cid > Set to 0000 > > can you reply please? > > Thank you, > Hoikeun > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, 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. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, 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. For more options, visit https://groups.google.com/d/optout.
