I need help with silac search using a a combined file from xtandem and comet

[sudarshan kumar]

Can anyone please extend help to me in SILAC run analysis using ASAPratio and express

I am facing problem at 

1. Xtandem search with two files. It is taking too much time and doestnt move ahead  after a few hours.

[sudarshan kumar]

in the tutorial page, In ASPARatioit shows-  a.      In the “XPRESS Options” pane select “RUN XPRESS”. 

                                          i.     Change “XPRESS Mass Tolerance” to 0.1,

                                         ii.     Set “Change XPRESS residue mass difference:” with K 8.0142 and R 10.0083.

                                       iii.     Set “Number of isotopic peaks to sum…” to 1

b.      In the “ASAPRatio Options” pane select “RUN ASAPRatio”.

                                          i.     Change “Labeled Residues” to K and R,

                                         ii.     Set “m/z range to include in summation of peak:” to 0.05.

                                       iii.     Check the “Use fixed scan range for Light and Heavy” option.

                                       iv.      set “Min iProphet Probability for Quantitation:” to 0.9

                                         v.     Set “Specified masses:” to K 136.10916 and R 166.10941.  

first of all, I couldnot find this "specified masses" tab

When I did it in static masses, the command failed to quantitate ASPARtio.

It says Lysine cannot be  both in variable modification and static modification.

Please suggest. though I am running the files without static modification.