Proton transfer reaction mass spectrometry (PTR-MS) is a technique for online measurements of atmospheric concentrations, or volume mixing ratios, of volatile organic compounds (VOCs). This paper gives a detailed description of our measurement, calibration, and volume mixing ratio calculation methods, which have been designed for long-term stand-alone field measurements by PTR-MS. The PTR-MS instrument has to be calibrated regularly with a gas standard to ensure the accuracy needed in atmospheric VOC measurements. We introduce a novel method for determining an instrument specific relative transmission curve using information obtained from a calibration. This curve enables consistent mixing ratio calculation for VOCs not present in a calibration gas standard. Our method proved to be practical, systematic, and sensitive enough to capture changes in the transmission over time. We also propose a new approach to considering the abundance of H₃O⁺H₂O ions in mixing ratio calculation. The approach takes into account the difference in the transmission efficiencies for H₃O⁺ and H₃O⁺H₂O ions. To illustrate the functionality of our measurement, calibration, and calculation methods, we present a one-month period of ambient mixing ratio data measured in a boreal forest ecosystem at the SMEAR II station in southern Finland. During the measurement period 27 March–26 April 2007, the hourly averages of the mixing ratios were 0.051–0.57 ppbv for formaldehyde, 0.19–3.1 ppbv for methanol, 0.038–0.39 ppbv for benzene, and 0.020–1.3 ppbv for monoterpenes. The detection limits for the hourly averages were 0.020, 0.060, 0.0036, and 0.0092 ppbv, respectively.