PQD, a new patented fragmentation mechanism, is now available on Thermo's 2D linear ion traps, eliminating the "1/3 Rule" or “Low Mass Cut-Off” for MS/MS data. Use of PQD allows for trapping and analysis of structure-informative ions such as b-1, y-1 and immonium ions. PQD also enables the detection of MS/MS reporter ions from isobaric peptide tags such as iTRAQ.
PQD is a novel fragmentation mechanism developed for the LTQ that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected. PQD fragmentation produces precise, reproducible fragmentation and has been used for iTRAQ peptide quantitation on the LTQ using both electrospray and MALDI source ionization.
PQD fragmentation of peptides produces robust precursor ion fragmentation, and provides the ability to routinely scan product ions down to m/z 50. Fragmentation occurs in about the same time scale as Collision Induced Dissociation (CID) and can easily be incorporated into general Xcalibur methods and used in conjunction with collision-induced dissociation (CID), MSn, and other scan functions.
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