Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is widely used for quantitative proteomic investigations. The typical output of such studies is a list of identified and quantified peptides. The biological and clinical interest is, however, usually focused on quantitative conclusions at the protein level. Furthermore, many investigations ask complex biological questions by studying multiple interrelated experimental conditions. Therefore, there is a need in the field for generic statistical models to quantify protein levels even in complex study designs.
protein quantification quantitative proteomics label-free lc-ms/ms linear mixed effects models statistical design of experiments