Longitudinal Plasma Protein Profiling Using Targeted Proteomics and Recombinant Protein Standards

Spike-in of standards of known concentrations
used in proteomics-based
workflows is an attractive approach for both accurate and precise
multiplexed protein quantification. Here, a quantitative method based
on targeted proteomics analysis of plasma proteins using isotope-labeled
recombinant standards originating from the Human Protein Atlas project
has been established. The standards were individually quantified prior
to being employed in the final multiplex assay. The assays are mainly
directed toward actively secreted proteins produced in the liver,
but may also originate from other parts of the human body. This study
included 21 proteins classified by the FDA as either drug targets
or approved clinical protein biomarkers. We describe the use of this
multiplex assay for profiling a well-defined human cohort with sample
collection spanning over a one-year period. Samples were collected
at four different time points, which allowed for a longitudinal analysis
to assess the variable plasma proteome within individuals. Two assays
toward APOA1 and APOB had available clinical data, and the two assays
were benchmarked against each other. The clinical assay is based on
antibodies and shows high correlation between the two orthogonal methods,
suggesting that targeted proteomics with highly parallel, multiplex
analysis is an attractive alternative to antibody-based protein assays.