Improved methods of tandem mass spectrometry for proteomics applications in a quadrupole ion trap mass spectrometer

Tandem mass spectrometry (MS/MS) in the quadrupole ion trap mass spectrometer has become a standard practice for the structural elucidation of peptides for proteomics research. In the quadrupole ion trap mass spectrometer, MS/MS is commonly effected using collision induced dissociation (CID). However, other methods of ion activation, such as infrared multi-photon photodissociation (IRMPD) have been used to dissociate parent ions in the quadrupole ion trap. The process of MS/MS has several limitations resulting from the operation of the quadrupole ion trap mass spectrometer. Two of these limitations are addressed in the research reported in this dissertation.; The first limitation addressed in this research is the loss of structural information resulting from product ions not trapped during the process of CID. During CID in the quadrupole ion trap, product ions with a mass-to-charge approximately one-fourth that of their parent ion's mass-to-charge are not trapped for mass analysis. A method of MS/MS termed High Amplitude Short Time Excitation (HASTE) CID has been developed to allow trapping of these lower mass-to-charge product ions. This method increases the structural elucidation of peptides by providing valuable information in the form of immonium ions that are not mass analyzed using conventional CID methods.; The second limitation to MS/MS addressed in this dissertation is that of dissociating multiple parent ions simultaneously. A method termed Iterative Accumulation Multiplexing (IAM) has been developed to increase the number of ions that can be identified during a single activation event. Using IAM, more than two parent ions can be simultaneously encoded, dissociated, and their resulting product ions identified from a ratiogram. Previous experiments conducted using IAM with CID were limited to a narrow range of qz values for the parent ions. However, other MS/MS techniques such as thermally assisted (TA) CID, IRMPD, and TA-IRMPD, the range of qz values at which a parent ion can be successfully activated during IAM is shown to increase. The increased range of qz values allow more product ions to be identified from the ratiogram, resulting in greater structural elucidation for the peptide parent ions.