Abstract. Mass spectrometric measurement of DMS by atmospheric pressure ionization with an isotopically labeled standard (APIMS-ILS) is a sensitive method with sufficient bandpass for direct flux measurements by eddy correlation. Use of an isotopically labeled internal standard greatly reduces instrumental drift, improving accuracy and precision. APIMS-ILS has been used in several recent campaigns to study ocean-atmosphere gas transfer and the chemical budget of DMS in the marine boundary layer. This paper provides a comprehensive description of the method and errors associated with DMS flux measurement from ship platforms. The APIMS-ILS instrument used by most groups today has a sensitivity of 100–200 counts s⁻¹ pptv⁻¹, which is shown to be more than sufficient for flux measurement by eddy covariance. Mass spectral backgrounds (blanks) are determined by stripping DMS from ambient air with gold. The instrument is found to exhibit some high frequency signal loss, with a half-power frequency of ≈1 Hz, but a correction based on an empirically determined instrument response function is presented. Standard micrometeorological assumptions of steady state and horizontal uniformity are found to be appropriate for DMS flux measurement, but rapid changes in mean DMS mixing ratio may serve as a warning that measured flux does not represent the true surface flux. In addition, bias in surface flux estimates arising from the flux divergence is not generally significant in the surface layer, but under conditions of lowered inversion and high flux may become so. The effects of error in motion corrections and of vertical motion within the surface layer concentration gradient are discussed and the estimated maximum error from these effects is ≤18%.