MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.
We plan to implement an automatic submission of the experiments in MaxQB to PRIDE, so that MaxQB data are also available in the databases that are part of ProteomeXchange. But Additionally, MaxQB features a number of analysis tools that are not currently present in other databases. For example, we here introduced a procedure to adjust the required cutoff scores to keep the overall false positive rate constant when incremental proteome projects are added. These analysis tools can be used in MaxQB, but they could also be incorporated into other proteome databases.