We present a new, off-line breath collection and analysis method, suitable for large screening studies. The breath collection system is based on the guidelines of the American Thoracic Society for the sampling of exhaled NO. Breath containing volatile gases is collected in custom-made black-layered Tedlar bags and analyzed by proton-transfer reaction mass spectrometry (PTR-MS). The collection method and data analysis is validated for its accuracy, precision, selectivity, limits of detection, sensitivity and reproducibility. Consecutive fillings of five bags by the same person gave reproducible results to within 12% relative standard deviation (RSD) for methanol, acetaldehyde, acetone and water content from breath, whereas isoprene was constant to within 30% RSD. In an exploratory small-scale case-control study, we monitor the exhaled breath of 11 lung cancer patients on the day before surgery. The control group consisted of 57 age-matched subjects, the so-called 'healthy smokers'. This study is used as an example of the use of the system presented here.