The Agilent G2722AA Spectrum Mill Extractor for Thermo Fisher Scientific Ion Trap Data Files is a collection of tools for high-throughput processing of MS and MS/MS spectra to provide protein and peptide identifications and relative quantitation. It enables the use of the time-saving Spectrum Mill workbench with LCQ, LTQ, LTQ FT, and LTQ Orbitrap *.raw files. It extracts and merges nearby MS/MS spectra from the same precursor ion (supports numerous modes, such as CID and ETD), optionally merges MS2 and MS3 spectra from the same precursor ion, assigns precursor charges where possible, calculates spectral features used in other Spectrum Mill programs, filters MS/MS spectra by quality, and enables quantitation by calculating extracted ion chromatograms from the intervening MS precursor scans.