Title :
A normalization method for multiple reaction monitoring (MRM) data
Author :
Jungsoo Gim ; Taesung Park
Author_Institution :
Dept. of Stat., Seoul Nat. Univ., Seoul, South Korea
Abstract :
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.
Keywords :
biochemistry; biological techniques; cellular biophysics; mass spectra; proteins; proteomics; MRM data; MRM experimental accuracy; MRM experimental reproducibility; MRM expression change quantification; MRM expression normalization step; SRM assay; SRM data; SRM experimental accuracy; SRM experimental reproducibility; SRM expression change quantification; SRM expression normalization step; accurate protein normalization; accurate protein quantification; biomarker discovery; biomarker identification platform; biomarker verification platform; candidate biomarker identification; candidate biomarker verification; differential expression analysis; differential expression inference; mass spectra; multiple reaction monitoring data; protein expression; real data sets; sample normalization method; selected reaction monitoring data; simulated data sets; Cancer; Data models; Monitoring; Peptides; Proteins; Proteomics; differential expression test; normalization; proteomics; selected reaction monitoring (SRM);
Conference_Titel :
Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on
Conference_Location :
Belfast
DOI :
10.1109/BIBM.2014.6999378
