Bottom up proteomics data analysis strategies to explore protein modifications and genomic variants

The quest to understand biological systems requires further attention of the scientific community to the challenges faced in proteomics. In fact the complexity of the proteome reaches uncountable orders of magnitude. This means that significant technical and data-analytic innovations will be needed for the full understanding of biology. Current state of art MS is probably our best choice for studying protein complexity and exploring new ways to use MS and MS derived data should be given higher priority. We present here a brief overview of visualization and statistical analysis strategies for quantitative peptide values on an individual protein basis. These analysis strategies can help pinpoint protein modifications, splice, and genomic variants of biological relevance. We demonstrate the application of these data analysis strategies using a bottom-up proteomics dataset obtained in a drug profiling experiment. Furthermore, we have also observed that the presented methods are useful for studying peptide distributions from clinical samples from a large number of individuals. We expect that the presented data analysis strategy will be useful in the future to define functional protein variants in biological model systems and disease studies. Therefore robust software implementing these strategies is urgently needed.