Organic compounds were measured by proton transfer reaction‐mass spectrometry (PTR‐MS) on board the National Oceanic and Atmospheric Administration's research ship Ronald H. Brown during the New England Air Quality Study (NEAQS) in July and August of 2002. PTR‐MS has the potential to measure many important organic species with a fast time response, but its validity has not been proven sufficiently. The results obtained by PTR‐MS during NEAQS were compared with those from (oxygenated) hydrocarbon measurements by gas chromatography/mass spectrometry (GC‐MS), peroxyacyl nitrate measurements by gas chromatography/electron capture detection, and carboxylic acid measurements by mist chamber/ion chromatography. The PTR‐MS and GC‐MS data for methanol, acetonitrile, acetone, isoprene, benzene, and toluene agreed within the measurement uncertainties. The comparison for C8 aromatics and acetaldehyde was less quantitative due to calibration inaccuracies. In addition, PTR‐MS measured the sum of methyl vinyl ketone and methacrolein at 71 amu, the sum of C9 aromatics at 121 amu, and the sum of monoterpenes at 81 and 137 amu. The PTR‐MS signal at 61 amu was found to correlate well with data for acetic acid. The signal at 73 amu correlated reasonably well with methyl ethyl ketone data, but the quantitative disagreement suggested interference from other species, possibly methyl glyoxal. The signal at 77 amu correlated well with data for peroxyacetyl nitrate, and the sensitivity inferred from the field data agreed within 30% with the results from laboratory calibrations. Finally, the signal at 105 amu was attributed to styrene and peroxy isobutyryl nitrate. These results prove that many important organic species can be measured accurately and with a fast response time by PTR‐MS.