Multiplexed MS/MS on a Quadrupole Ion Trap Mass Spectrometer

The Quadrupole Ion Mass Spectrometer (QITMS) is used extensively in proteomics research. It provides primary sequence information for proteins and peptides and can be used to rapidly and sensitively identify proteins in complex mixtures when coupled with high-performance liquid chromatography (HPLC). For very complex mixtures like those increasingly found in proteomic and quantitative proteomics analyses, a major limitation of the QITMS is its difficulty with rapidly analyzing multiple compounds simultaneously. The novel aspect of this invention is a new encoding scheme that will allow the existing QITMS to be extended to permit multiple compounds to be analyzed concurrently, which will dramatically improve sample throughput and facilitate proteomics research. The encoding scheme allows the parent/product ion relationships to be easily determined after isolation and dissociation of multiple ions, providing a link between parent ions and their product ions by encoding parent ion abundances in a known way from the first product ion spectrum to the second.