A fundamental challenge lies in the calibration of vendor-specific arbitrary intensity units into a universal metric. In an ideal world, we could inject a fixed amount of analyte to allow direct comparisons of the number of ions reaching the detector to compare between different MS instruments. To address this gap, we present a strategy that uses the relationship between the number of ions measured and the precision to derive a correction factor between the intensity reported by the vendor as a metric in ions/sec. We use this calibration factor to compare between different instrument platforms, and we show that Thermo Scientific linear ion traps report an intensity that is well calibrated to ions/sec, whereas orbitrap analyzers need to be divided by a 10-15x to obtain the same measurement. We integrated this ion-counting framework into Skyline by leveraging the signal intensity and injection time to measure the ion count for each peptide. We implement the calibration protocol in an app that will ultimately become a Skyline external tool. Furthermore, we implemented new metrics into the Skyline document grid that can be used to evaluate both targeted and untargeted proteomics measurements.