Abstract
Parsimony and protein grouping are widely employed to enforce economy in the number of identified proteins, with the goal of increasing the quality and reliability of protein identifications; however, in a counterintuitive manner, parsimony and protein grouping may actually decrease the reproducibility and interpretability of protein identifications. We present a simple illustration demonstrating ways in which parsimony and protein grouping may lower the reproducibility or interpretability of results. We then provide an example of a data set where a probabilistic method increases the reproducibility and interpretability of identifications made on replicate analyses of Human Du145 prostate cancer cell lines.