Longitudinal Plasma Protein Profiling Using Targeted Proteomics and Recombinant Protein Standards

David Kotol, Helian Hunt, Andreas Hober, Max J. Karlsson, Björn Forsström, Anders Gummesson, Göran Bergström, Linn Fagerberg, Mathias Uhlén, Fredrik Edfors*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


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.
Original languageEnglish
JournalJournal of Proteome Research
Issue number12
Pages (from-to)4815-4825
Number of pages11
Publication statusPublished - 2020


  • Mass spectrometry
  • Proteomics
  • Blood plasma
  • Stable isotope standards
  • Absolute quantification
  • Recombiant protein standards
  • Precision medicine


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