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Modern mass spectrometers are now capable of producing tens of thousands of tandem mass (MS/MS) spectra per hour of operation, resulting in an ever-increasing burden on the computational tools required to translate these raw MS/MS spectra into peptide sequences.

To address this need, we have developed a new program, MacroSEQUEST, which exhibits a dramatic improvement in processing speed by transiently indexing the array of MS/MS spectra prior to searching FASTA databases.

This new program also extends the capability of SEQUEST by implementing a parameter that allows for scalable sparse arrays of experimental and theoretical spectra to be implemented for high-resolution correlation analysis and demonstrate the advantages of high-resolution MS/MS searching to the sensitivity of large-scale proteomics data sets.
Visit the SourceForge repository here.