Stable isotope-labeled standard (SIS) peptides used in targeted proteomics workflows provide robust protein quantification, which is required in a clinical setting. However, SIS peptides are typically added post trypsin digestion and can vary significantly between experiments and also within a protein. This can lead to uncertain quantification as both the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments. These standards are added initially to the sample and SIS peptides are released upon trypsin digestion. The PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. In this study, an automated and scalable sample preparation workflow was established that enabled simultaneous preparation of up to 96 samples. Robust quantification of 13 apolipoproteins was achieved by a novel multiplex SIS protein fragment-based LC-SRM/MS assay performed on non-depleted human plasma was achieved. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) across all apolipoproteins and was subsequently utilized to investigate the effects of omega-3 carboxylic acids (OM3-CA) and fenofibrate. The proteins were quantified in a cohort consisting of a randomized placebo-controlled trial ( EFFECT I, NCT02354976). No significant changes were observed in the OM3-CA arm, while treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS protein fragments can facilitate the generation of robust multiplexed biomarker assays for absolute quantification of proteins in clinical studies.