Mass spectrometry–based targeted proteomics allows objective protein quantitation of clinical biomarkers, including from formalin-fixed, paraffin-embedded (FFPE) human tumor biopsies. Each tumor biopsy is a distinct complex matrix, with potential for interference with the target peptide fragment ions. The combination of stable-isotope labelled internal standard (SIS) peptides and high-resolution detection in a parallel reaction monitoring experiment mitigates the interference problem. We deploy a novel data analysis pipeline allowing: 1) narrow extraction windows in the retention time dimension; 2) reporting the differences of the deviations from the expected m/z values, between SIS and target peptide fragment ions to flag possible interference. We highlight the benefits of this approach compared to the widely used Skyline platform for complex FFPE tissue sample sets.
ThOB pm: Biomarkers: Quantitative Analysis – PRM-Studio: Improved data extraction and quality control of peptide PRM data for complex clinical samples
by Eva Bryderup