bookmark MS-REDUCE An algorithm for ultrafast reduction of MS/MS data in pre-processing stage. The proposed algorithm is a low-complexity procedure based on random sampling, approximate classification and quantization making it highly scalable with increasing number of spectra. MS-REDUCE is capable of eliminating noisy peaks as well as peaks that do not contribute to peptide deduction before any peptide deduction is attempted. Our experiments have shown up to 100× speed up over existing state of the art noise elimination algorithms while maintaining comparable high quality matches. Using our approach we were able to process a million spectra in just under an hour on a moderate server.