Table 3:

Designating DMPK/PD applications using a tiered, fit-for-purpose approach

	Characteristics	DMPK/PD applications	Optimum LC-MS approaches
Tier 1: Precise and accurate assays	• Absolute protein quantification • The ability to measure repeatedly sets of analytes of interest within and across samples/experiments (A) • These assays employ internal standards for each analyte, for confident detection and precise quantification (B). • High level of validation required	• Protein complex stoichiometry (hetero-complexes) • Systems biology and QSP modelling • Cross-laboratory comparison • Quantification and comparison of multiple proteins in different samples • Assessment of isoform distribution and allelic variants • Long-term use of historical protein abundance data in PBPK modeling • Protein networks and alterations in disease	• MRM/PRM using PSAQ standards • MRM using AQUA/QconCAT standards
Tier 2: Precise assays	• Characteristics A and B	• Use in PBPK modeling and IVIVE • Protein biomarker analysis • Inter-experiment comparison • Induction/suppression of abundance relative to control condition • Inter-organism differences	• MRM/PRM using AQUA/QconCAT standards • Global TPA
Tier 3: Semi-quantitative assays	• High-throughput (shotgun proteomics) • High coverage	• Method development • Semi-quantitative analysis • Regional and sub-cellular localization of proteins • Biomarker discovery	• Discovery-scale DDA, DIA/SWATH