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The early stages of fibril formation are difficult to capture in solution. We use cold-ion spectroscopy to examine an 11-residue peptide derived from the protein transthyretin and clusters of this fibre-forming peptide containing up to five units in the gas phase. For each oligomer, the UV spectra exhibit distinct changes in the electronic environment of aromatic residues in this peptide compared to that of the monomer and in the bulk solution. The UV spectra of the tetra- and pentamer are superimposable but differ significantly from the spectra of the monomer and trimer. Such a spectral evolution suggests that a common structural motif is formed as early as the tetramer. The presence of this stable motif is further supported by the low conformational heterogeneity of the tetra- and pentamer, revealed from their IR spectra. From comparison of the IR-spectra in the gas and condensed phases, we propose putative assignments for the dominant motif in the oligomers.

The accurate and unambiguous detection of post translational modifications in proteins and peptides remains a challenging task. We report here the use of cold ion spectroscopy for the identification of phosphorylated tyrosine residues in peptides. This approach employs the wavelength specific UV fragmentation of cryogenically cooled protonated peptides in the gas phase. In addition to the appearance of specific photofragments the phosphorylation of tyrosine induces large spectral shifts of the peptide electronic band origins. Quantum chemical calculations and experiments together suggest a certain generality of the use of such shifts in the spectroscopic identification of phosphotyrosines. The enhanced selectivity offered by the joint application of wavelength specific fragmentation and mass spectrometry of cold molecules can also be used in the identifications of aromatic residues in protonated peptides and potentially of other UV absorbing groups in a variety of large polyatomic ions. © 2014 American Chemical Society.

Keywords: spectroscopy, peptides, cold ion traps, mass spectrometry Reference EPFL-ARTICLE-164212doi:10.1002/anie.201100702View record in Web of Science Record created on 2011-03-11, modified on 2017-11-27

Dimethylaminonitrene complexes of IMesM(+) (IMes =1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene; M = Cu, Ag, Au) were prepared in the gas phase and structurally characterized by high-resolution infrared spectroscopy of the cold species, ion-molecule reactions, and DFT computations. We measured the binding energies of the nitrene fragment to the IMesM(+) moiety by energy-resolved collision-induced dissociation experiments in the gas phase, affording a trend in bond strength of M = Cu ≈ Au > Ag. This trend is explained in terms of a detailed metal-nitrogen bonding analysis, from which relativistic effects on the bonding were assessed. Various density functionals were evaluated for reproducing the observed thermochemical data and Truhlar's M06 functional was found to give the best agreement.

We have measured a vibrationally resolved UV spectrum of doubly protonated gramicidin S (GS) in the gas phase and, subsequently, a highly resolved, conformer-specific IR spectrum in the 6 mum fingerprint region, using a cold ion trap in combination with table-top lasers. The study has revealed at least three conformational states of GS populated under our experimental conditions, with the major one showing evidence of a symmetric three-dimensional structure similar to that in the condensed phase. The derived qualitative constraints, along with the measured vibrational frequencies, serve as a benchmark for computations of peptide structure.

Spectroscopic fingerprint: Infrared–ultraviolet double resonance photodissociation is used for conformational assignment of the electronic spectra of a cold protonated decapeptide (see picture). A mechanism of the IR–UV depletion spectroscopy is proposed and a procedure of using it for measurements of absolute absorption cross-sections of vibrational transitions is elaborated.