Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. - Timothy Clough; Safia Thaminy; Susanne Ragg; Ruedi Aebersold; Olga Vitek (BMC Bioinform., 2012)

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. - Meena Choi; Ching-Yun Chang; Timothy Clough; Daniel Broudy; Trevor Killeen; Brendan MacLean; Olga Vitek (Bioinform., 2014)