The paper describes a high-performance rcconfigurable computing solution for real-time peptide mass fingerprinting. The FPGA system can process the raw mass spectrum generated by a MALDI-ToF mass spectrometer and perform a search against the entire MSDB database in 240 ms. This represents an almost 2000 fold speed up compared with an equivalent software implementation in C, running on a single 3 GHz Xeon workstation.