Real-time evaluation of experimental variation in large-scale LC–MS/MS-based quantitative proteomics of complex samples

Quantitative proteomic profiling is becoming a widely used approach in systems biology and biomarker discovery. There is a growing realization that quantitative studies require high numbers of unpooled samples for increased statistical power. Large-scale quantitative analyses require an added degree of stringency due to the lengthy study periods and reliance on stability of analytical instrumentation. We present the inclusion of quality control samples alongside clinical samples in the preparation and nanoLC–MS analysis pipelines. These serve the purpose of monitoring, evaluating and reporting experimental variation measured in real-time. This concept is shown for two types of complex biological samples: serum samples and fibroblast samples. In both studies QC samples were added among dozens of clinical ones and analyzed using a label-free quantitative proteomic platform.