Quadrupole ion trap mass spectrometry of peptides

Citation

Jonscher, Karen Rae (1997) Quadrupole ion trap mass spectrometry of peptides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/9btc-bk47. https://resolver.caltech.edu/CaltechETD:etd-01142008-075423

Abstract

Biological mass spectrometry addresses the challenging unsolved structural issues surrounding biopolymers of fundamental importance to the biomedical sciences. Key to this discipline is the ability to extract useful information from complex peptide mixtures. Several approaches were developed to analyze peptides utilizing the unique capabilities of the quadrupole ion trap mass spectrometer. An external matrix-assisted laser desorption ionization source was constructed. Detection of peptides in the mid-femtomole range and of proteins in the low-femtomole range was reported. Singly-charged molecules with molecular weights in excess of 34,000 u were observed. Peptides generated by enzymatic digestion of the P protein of Sendai virus were separated by HPLC and the technique was successfully applied to locate phosphorylation sites.

A hybrid quadrupole mass filter/quadrupole ion trap mass spectrometer was assembled. Peptide mixtures were separated by sequentially transmitting one value of m/z into the ion trap for mass analysis. The sequential injection technique served to significantly reduce space charge-induced suppression effects and improved resolution and fragmentation efficiency when compared to results obtained using an ion trap. A novel method of scanning afforded the ability to perform neutral loss experiments for the identification of phosphopeptides in a mixture. A long duty cycle, due to acquisition hardware, limited the utility of this approach for continuous ionization techniques.

A low flowrate ionization source was constructed and interfaced to the hybrid and to an ion trap. A unique needle configuration provided a detection limit of 75 attomole of a peptide mixture infused into the source. A new type of liquid junction was developed to apply voltage to the sample consisting of a platinum wire inserted into the sidewall of a length of Teflon tubing. The junction was versatile, robust, and easy to use and performance compared well with other types of junctions. Capillary electrophoresis and hydrophobic membranes were used to separate peptide mixtures. Detection limits of the techniques were 1 femtomole and 10 femtomoles, respectively, for angiotensin. Differential release of peptides using step elutions from the hydrophobic membrane was demonstrated, providing a sensitive, high throughput means of mixture simplification prior to separation by capillary electrophoresis.

Thesis Files