Clauser originated the Spectrum Mill suite of software tools for high-throughput interpretation of discovery-mode LC-MS/MS datasets to provide protein/peptide/PTM identification and quantitation, and he also contributes to its ongoing development with Broad partner Agilent Technologies Inc. Recent software development efforts have focused on detection of single amino acid variant and splice isoforms; scoring the certainty/ambiguity in modification site localization; relative quantitation from isotope encoding experiments (i.e. iTRAQ/TMT and SILAC); false discovery rate calculation; and quality metrics for measuring performance aspects of mass spectrometry, chromatography, spectral interpretation, and sample handling.