Proton Transfer Reaction Time of Flight Mass Spectrometry (PTR-ToF-MS) is a direct injection MS technique, allowing for the sensitive and real-time detection, identification and quantification of volatile organic compounds (VOCs). When aiming to employ PTR-ToF-MS for targeted VOC analysis some methodological questions must be addressed, such as the need to correctly identify product ions, or evaluating the quantitation accuracy. This work proposes a workflow for PTR-ToF-MS method development, addressing the main issues affecting the reliable identification and quantification of target compounds. We determined the fragmentation patterns of 13 selected compounds (aldehydes, fatty acids, phenols). Experiments were conducted under breath-relevant conditions (100% humid air), and within an extended range of reduced electric field values (E/N = 48-144 Td), obtained by changing drift tube voltage. Reactivity was inspected using H3O+, NO+ and O2+ as primary ions. The results show that a relatively low (< 90 Td) E/N often permits to reduce fragmentation enhancing sensitivity and identification capabilities, particularly in the case of aldehydes using NO+, where a 4-fold increase in sensitivity is obtained by means of drift voltage reduction. We developed a novel calibration methodology, relying on diffusion tubes used as gravimetric standards. For each of the tested compounds, it was possible to define suitable conditions whereby experimental error, defined as difference between gravimetric measurements and calculated concentrations, was 8% or lower.