Hi James, I'm sure that what I do is the best way but it work for me pretty well: I make one X!tandem input for every search conditions I use and usually save them with the relevant data in the relevant data folder. You can start with X!tandem sample input file (downloaded form http://www.thegpm.org/TANDEM/api/eg.xml) add to it the k-score plugin settings: (http://tools.proteomecenter.org/wiki/index.php?title=TPP:X! Tandem_and_the_TPP) and your specific changes (Lys C etc). And when you will be asked for the parameter file specify this xml file. It will overrule the default parameter file of the TPP when specified. Good luck, Oded
On Jun 14, 2:10 am, James Dowell <[email protected]> wrote: > Hi, > > I am trying to set-up the TPP to run an X!Tandem search. I've read > Jimmy Eng's tutorial on using X!Tandem within the TPP. The problem > I'm having is editing the X!Tandem parameters file. Should I be > editing the default parameters file (tandem_params) in the parameters > folder? Or should I be creating a new parameters file in the data > folder? I'm trying to search data that needs the enzyme set to Lys-C > and I can't seem to find the protein cleavage input in the default > params file. > > Thanks, > James --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
