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

  • Fabian S. Menges
  • Evan H. Perez
  • Sean C. Edington
  • Chinh H. Duong
  • Nan Yang
  • Mark A. JohnsonEmail author
Research Article


We describe an instrumental configuration for the structural characterization of fragment ions generated by collisional dissociation of peptide ions in the typical MS2 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 D2 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 a1, y1 and z1 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 z1 ion, nominally formed after NH3 is ejected from the protonated tyrosine (y1) product, is identified as the cyclopropane-based product is tentatively identified as a cyclopropane-based product.


Cryogenic vibrational spectroscopy MS2 Peptide ion fragment structure Orbitrap High-resolution mass spectrometry 



MAJ thanks the Air Force Office of Scientific Research (AFOSR) under grants FA9550-17-1-0267 (DURIP) and FA9550-18-1-0213. CHD thanks the National Science Foundation Graduate Research Fellowship for funding under Grant No. DGE-1122492. FSM thanks Prof. David Russell and Michael Poltash (Texas A&M) for useful discussions about their adaptation of a Thermo Fisher Scientific Exactive Plus in combination with an external ion source and Henk Terink from Thermo Fisher Scientific for technical support. EHP thanks the support of the National Institute of Health for the stipend supported under the Biophysical Training Grant 2T32GM008283-31.

Supplementary material

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Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Department of ChemistryYale UniversityNew HavenUSA

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