Hi, I have encountered an issue wherein if I try to convert a mascot .dat file to pepxml, it does the conversion and when I try to use this pepxml to run peptideprophet and proteinprophet, it fails.
I tried to check if .dat to pepxml conversion worked properly, but realised that when I click on the pepxml, nothing loads on the pepxml viewer and I also saw that usually there is an index file that is created and in this case, it did not create the index file as well. Just to make sure the .dat file is good, i was also able to open it up on Scaffold and see some proteins. This is the link to the shared dropbox folder called "TPP" https://www.dropbox.com/sh/4unsley0gir7jve/7D3-XANnj8 I have 2 folders there, one called "working files" where I tested a .dat file (from same samle, different fraction) conversion to pepxml and ran peptide and protein prophet and it worked successfully. The other folder called "not working files" has the .dat file which failed to run peptide and protein prophet. Also attached are .mzxml, .pepxml, the log of conversion from .dat to .pepxml and errorlog of conversion from pepxml to peptide and protein prophet along with screenshots. I have also included the fasta file I used in the "Fasta" folder. Can you anyone guide me as to what could have gone wrong? Thanks in advance, Vidya -- 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/-/_OXYGwHUJmQJ. 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.
