I would set the Xpress mass tolerance to 1.0 for the LTQ data. In Sequest, 'peptide mass tolerance' is the mass tolerance for the calculated peptide mass, which is a function of MS1 precursor scan accuracy, while 'fragment ion tolerance' is the mass tolerance applied to the ms/ms fragment ions. The values you're using are reasonable. You might consider lowering the fragment mass tolerance to 0.5. There is a built-in minimum tolerance due to how the ms/ms peaks are internally represented so I actually use a 0.0 fragment mass tolerance in my searches but I don't use the commercial version from Thermo so I don't know if this 0.0 value would behave the same for you (although there is a decent chance it would).
On Wed, May 4, 2011 at 1:45 AM, 杨豫鲁 <yuluwy...@gmail.com> wrote: > Dear ： > > Hi, > > There is some question when I use the Xpress from Trans-Proteomic > Pipeline for analysis and validation of peptides and proteins ,which was > labeled by SILAC, after searching the raw files through sequest( Bioworks > Browser ,Thermo Fisher, San Jose, CA) against the NCBI RefSeq database of > human sequences. > > For the instrument we used was a LC-MS/MS（LTQ,Thermo),the sensitivity of > which is no good than that of LTQ-FT or LTQ-Orbitrap.How to set the ‘ > Change Xpress mass tolerance' in the Xpress Options ? And what's the > differense between it and the ' peptide tolerance'and 'Fragment ions > tolerance' in the Sequest Search Parameters? We set the peptide tolerance > as 2.0 amu and Fragment ions tolerance as 1.0 amu , are they reasonable with > regard to our LTQ ? > > Please return as soon as posssible. > > All yours > > -- > Yulu Yang > Ph.D Candidate > School of Life Science and Biotechnology > Shanghai Jiao Tong University > P.R. China > 86-21-34204875(office) -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
