Simon, To avoid the errors, convert to mzXML first and then use MzXML2Search to generate the mgf file. I don't have my work machine handy to verify but I assume that msconvert doesn't write mgf files in the same format that the TPP needs for full compatibility. Specifically the TPP expects specific information to be encoded in the TITLE line of the mgf files from where the underlying scan #s will be parsed.
- Jimmy On Sun, May 30, 2010 at 11:01 PM, Simon Michnowicz <[email protected]> wrote: > Dear Group, > I have encountered an error in Mascot2XML when processing a WIFF file > that had been converted to mgf (for a MascotSearch) and mzXML using > msconvert. > The program encounters an error, which exits and leaves behind a > partially-formed pepXML file. > > Mascot2XML simon-J2361.dat -D/mnt/sanfs/APCF/mascot/sequence/ > SwissProt/current/uniprot_sprot_April2010.fasta -Etrypsin -pI > > This produces a lot of warnings of the kind: > > "Warning: could not find scan numbers of spectrum scan=6087 > > Set to 0000" > > > and then an error message > Replacing 6217 protein id with full ids by parsing through the > database... > searching /mnt/sanfs/APCF/mascot/sequence/SwissProt/current/ > uniprot_sprot_April2010.fasta.....5%.....10%.....15%.....20%..... > 30%.....35%.....40%.....45%.....50%. > ....60%.....65%.....70%.....75%.....80%.....90%.....95%...done > 575. opening scan=6034.out > error: only found 0 periods in scan=5771 > > > Can anyone assist me in this matter? > Thanks > Simon Michnowicz > > -- > 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. > > -- 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.
