If you know the fragmentation pattern of your peptides then you can search for these in either MRM or SRM mode. I presume you have some pure peptide that you will be analysing for? in order to quantitate you will need this. Hope this helps
I have quantified 19 kDa protein in the snail blood samples with LC-ESI-TOF instrument. You can find detailed information here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138787