Recommendations for Peptides Used In Mass Spectrometry Assays

Hoofnagle, A.N.; Whiteaker, J.R.; Carr, S.A.; et al.

Clinical laboratories are beginning to employ bottom-up MS-based methods with stable isotope-labeled standards for protein quantitation of biosamples, yet the procedures for development (from peptide selection to handling) and analysis are not well standardized. This report provides a compendium of guidelines and specifications from experts in the field for effectively using internal peptide standards to quantify endogenous peptides in complex proteolytic sample digests. The goal of the recommendations is to achieve precise, relative quantitation that can be harmonized across laboratories with high a degree of repeatability/reproducibility.