The present invention provides a method for identifying biomarkers and generating an output indicative of disease. The method for identifying biomarkers comprises the steps of collecting a breath sample from subjects known to have a disease and subjects known to be free of the disease； analyzing the collected breath samples to determine all mass ions in each of the collected breath samples using at least one time-resolved separation technique and at least one mass-resolved separation technique； identifying a subset of the determined mass ions in a processor as the biomarkers for detecting the disease, the subset of the determined mass ions are statistically significant for detecting the disease； and combining the subset of the determined mass ions in a multivariate algorithm in the processor to generate a value of a discriminant function indicating the likelihood that the subject has the disease.
