Integration of High-Resolution Mass Spectrometry with Cryogenic Ion Vibrational Spectroscopy

We describe an instrumental configuration for the structural characterization of fragment ions generated by collisional dissociation of peptide ions in the typical MS 2 scheme widely used for peptide sequencing. Structures are determined by comparing the vibrational band patterns displayed by cryogenically cooled ions with calculated spectra for candidate structural isomers. These spectra were obtained in a linear action mode by photodissociation of weakly bound D 2 molecules. This is accomplished by interfacing a Thermo Fisher Scientific Orbitrap Velos Pro to a cryogenic, triple focusing time-of-flight photofragmentation mass spectrometer (the Yale TOF spectrometer). The interface involves replacement of the Orbitrap’s higher-energy collisional dissociation cell with a voltage-gated aperture that maintains the commercial instrument’s standard capabilities while enabling bidirectional transfer of ions between the high-resolution FT analyzer and external ion sources. The performance of this hybrid instrument is demonstrated by its application to the a 1 , y 1 and z 1 fragment ions generated by CID of a prototypical dipeptide precursor, protonated L-phenylalanyl-L-tyrosine (H + -Phe-Tyr-OH or FY-H + ). The structure of the unusual z 1 ion, nominally formed after NH 3 is ejected from the protonated tyrosine (y 1 ) product, is identified as the cyclopropane-based product is tentatively identified as a cyclopropane-based product.