In contrast to common expectations, the differences in limits of detection (LODs) between electron capture negative ionization (ECNI) and electron ionization (EI) mass spectrometry (MS) were found to be insignificant for a wide range of aldehydes derivatized with o- (2,3,4,5,6-pentafluorobenzyl)-hydroxylamine hydrochloride. Comparison of the two ionization methods based on LOD confidence intervals revealed that a traditional presentation of the LOD or limit of quantitation (LOQ) as a single value may over/underestimate the significance of obtained results. LODs were between 20 and 150 pg injected for the majority of tested derivatized carbonyls using both ionization methods. ECNI-MS improved LODs by ϳ10-to 20-fold only for two derivatized aldehydes, 4-hydroxybenzaldehyde and 5-(hydroxymethyl)furfural. Selectivity of ECNI did not appear to be beneficial when analyzing a wood smoke particulate matter (WS-PM) extract, possibly because the majority of interferences were removed during sample preparation (i.e., liquid-liquid extraction). The impact of four different data acquisition modes of transmission quadrupole (TQ)-MS on LODs and their precisions was also investigated. As expected, LODs in the selected ion monitoring (SIM) were ϳtwo to four times lower than those obtained using total ion current (TIC) mode. More importantly, TQ-MS in the selected ion-total ion (SITI) mode (i.e., acquiring SIM and TIC data in a single analysis) provided signal-to-noise ratios and precisions, which were comparable to SIM alone. (J Am Soc Mass Spectrom 2010, 21, 592-602)