MaSpeQC: An easy-to-use Interactive Pipeline to Assess the Performance of LC-MS/MS Instrumentation

Mass spectrometers and their attached liquid chromatography (LC) systems, often referred to as LC-MS/MS instrumentation, have become an indispensable tool in biomedical research to identify and quantify proteins, metabolites, and other molecules of interest. However, these sophisticated instruments are very susceptible to malfunction or suboptimal performance, and as a result, quality control (QC) samples are typically acquired at regular intervals to assess their performance. Not surprisingly, several QC software packages have been developed in recent years to analyze and interrogate a variety of QC samples. However, existing QC software predominantly supports proteomic QC samples, with limited options for metabolomic and lipidomic QC samples. In addition, pipelines and workflows that can accommodate both types of QC samples are largely missing. To address this unmet demand, we have developed MaSpeQC, which is a free, easy-to-install, interactive and fully customizable web application to track LC-MS/MS performance across proteomic, metabolomic, and/or lipidomic workflows. MaSpeQC is vendor-agnostic and can handle any commercially available or in-house-generated QC sample from which it extracts relevant metrics. Furthermore, MaSpeQC provides an intuitive web interface for performance monitoring and early detection of issues through customizable email alerts.