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. T
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 databas
