Newby with X!Tandem and TPP

[rprambo]

Hi,

I am new to MS analysis. I am analyzing ms data from one organism -
fractionated lysate type material. I converted the data format
(*.RAW) to mzXML using msconvert (worked great!) and now am ready to
perform the database search using X!Tandem (or OMSSA). It seems the
workflow after the search is to use Peptide Prophet then Protein
Prophet.

Do I have to do a decoy database at any point?

And also, I am interested in doing spectral counting. Is there an
uncertainty or standard deviation associated with this count?

Thanks,

Rob R.