A quick guideline for PRM method development applied to target proteomics in biological fluids

Combining in-silico analysis, serum high abundant protein depletion, and DDA and PRM acquisitions, we established a simple workflow to select PRM high response peptides for protein quantification in serum. The workflow enables evaluating peptide intensity, MS2 match with the spectral library, peptide stability, and linearity of response to different injected masses. This workflow was successfully applied to twelve human complement system proteins. Besides, we employed synthetic labelled peptides to compensate inter LC-MS run variability, improving the quantification. We could demonstrate this method is useful and applicable for quantification of diverse targets with time optimization and accuracy insurance by quantitative proteomics technology.