Preliminary comparison of precursor scans and liquid chromatography-tandem mass spectrometry on a hybrid quadrupole time-of-flight mass spectrometer.

Recent mass spectrometry instrumentation developments include the appearance of novel hybrid tandem instrumentation, Q-TOF, consisting of a quadrupole mass analyzer (MS1) and a time-of-flight (TOF) analyzer. The TOF analyzer is not scanned, but collects all fragment ions entering the analyzer at a given time. Thus, the typical precursor scan experiment cannot be performed. Instead, a full MS-MS spectrum can be acquired for each mass passed by MS1. Appropriate data manipulation, i.e. extracted ion current chromatograms, can correlate specific fragment ion formation to the parent ion. Precursor scanning and LC-MS-MS are compared on a Q-TOF instrument for the determination of protein modifications, including acetylation and phosphorylation. Model peptides used for phosphopeptide detection were generated from a mixture of beta-casein. Model acetylated peptides were generated from a mixture of acetylated substance P1-9 and substance P1-11. The results were then applied to a more complex mixture, a digest of HIV-p24. Results indicate that precursor scanning is useful for screening, but that LC-MS-MS has a sensitivity advantage and is less susceptible to suppression effects. LC-MS-MS, therefore, appears to be better for the detection of trace components in complex mixtures.