Sorting protein lists with nwCompare: a simple and fast algorithm for n-way comparison of proteomic data files

MS, the reference technology for proteomics, routinely produces large numbers of protein lists whose fast comparison would prove very useful. Unfortunately, most softwares only allow comparisons of two to three lists at once. We introduce here nwCompare, a simple tool for n-way comparison of several protein lists without any query language, and exemplify its use with differential and shared cancer cell proteomes. As the software compares character strings, it can be applied to any type of data mining, such as genomic or metabolomic datalists.