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Troubleshooting liquid chromatography tandem mass spectrometry (LC-MS/MS) systems is a top priority in academic and commercial proteomics laboratories. We present a new software tool, MassQC, that builds on work from the National Institute of Standards and Technology (NIST) to provide an easy-to-use and powerful method to evaluate and track LC-MS/MS system performance over time. Using this novel approach we explore three common system failure modes (including spray instability, detector sensitivity degradation and erratic peptide elution) that were detected by MassQC while operating Thermo LTQ and LTQ-Orbitrap LC-MS/MS instruments. While viewing total ion current or base peak intensity may or may not shed light on these problems, MassQC alerts you to out-of-range metrics through robust trend tracking. Further, MassQC proved valuable for troubleshooting common system performance problems and optimizing LC-MS/MS instrument operation for improving proteomics reproducibility.