A normalization method for multiple reaction monitoring (MRM) data

High accuracy and reproducibility provided by selected or multiple reaction monitoring (SRM/MRM) experiments suggest that it is likely to become the platform of choice for identifying and verifying candidate biomarkers. Although several methods have been developed to quantify and discover the significant changes in SRM/MRM expression, we show normalization continues to be an essential step in the differential expression analysis. Here, we first investigate what makes normalization across the samples difficult in SRM assay. Then, we suggest a simple but effective normalization method to overcome the difficulty. Both real and simulated data sets are examined and improved results, compared to an existing method, are shown for inferring differential expression.