Generalized Linear and Mixed Models for Label-Free Shotgun Proteomics.

Label-free shotgun proteomics holds great promise, and has already had some great successes in pinpointing which proteins are up or down regulated in certain disease states. However, there are still some pressing issues concerning the statistical analysis of label-free shotgun proteomics, and this field has not enjoyed as much dedication of statistical research towards it as microarray research has. Here we reapply previously used statistical methods, the QSpec and quasi-Poisson, as well as apply the negative binomial distribution to both a control data set and a data set with known differential expression to determine the successes and failure of each of the three methods.