H/D exchange kinetics: Experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing

We report the use of unimolecular dissociation by infrared radiation for gaseous multiphoton energy transfer to determine relative activation energy (E a,laser ) for dissociation of peptide sequence ions. The sequence ions of interest are mass-isolated; the entire ion cloud is then irradiated with a continuous wave CO 2 laser, and the first order rate constant, k d , is determined for each of a series of laser powers. Provided these conditions are met, a plot of the natural logarithm of k d versus the natural logarithm of laser power yields a straight line, whose slope provides a measure of E a,laser . This method reproduces the E a values from blackbody radiative dissociation (BIRD) for the comparatively large, singly and doubly protonated bradykinin ions (nominally y 9 and y 9 2+ ). The comparatively small sequence ion systems produce E a,laser values that are systematic underestimates of theoretical barriers calculated with density functional theory (DFT). However, the relative E a,laser values are in qualitative agreement with the mobile proton model and available theory. Additionally, novel protonated cyclic-dipeptide (diketopiperazine) fragmentation reactions are analyzed with DFT. FT-ICR MS provides access to sequence ions generated by electron capture dissociation, infrared multiphoton dissociation, and collisional activation methods (i.e., b n , y m , c n , z m• ions).

Section: P Roduct Ions Formed By Tandem Mass Spectrometry (Ms/ Ms or Msmentioning

confidence: 99%

Section: P Roduct Ions Formed By Tandem Mass Spectrometry (Ms/ Ms or Msmentioning

confidence: 99%

Section: P Roduct Ions Formed By Tandem Mass Spectrometry (Ms/ Ms or Msmentioning

confidence: 99%

See 1 more Smart Citation

Relative Stability of Peptide Sequence Ions Generated by Tandem Mass Spectrometry

Bythell

Hendrickson

Marshall

2012

“…2-(denoted in bold-red font, Figure 1a). Numerous investigations of peptide ion scrambling indicate that fragment ions (e.g., b-type ions; Roepstorff and Fohlman's nomenclature [33]) generated during CID of peptide ions are themselves rearranged, and that the evidence of such rearrangements (i.e., Bscrambled^fragment ions) can be observed upon subsequent fragmentation [27,[34][35][36][37][38][39] ) could be produced from CID of intact 5′ phosphorylated DNA, we performed an analogous experiment to that presented in Figure 1a on a 5′ phosphorylated oligonucleotide (i.e., Oligo-2) with the same sequence as the last five nucleotides of Oligo-1 (i.e., p-GTA GA). Figure 1a and b) were present in both mass spectra, and with comparable fragment ion relative abundances.…”

Section: Resultsmentioning

confidence: 99%

DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

Harper

Neumann

Solouki

2015

Self Cite

Abstract. Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5′ phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5′ phosphate group in w type ions and 5′ phosphorylated DNA to generate sequence permuted [phosphopurine] -fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine] -and complementary y-B type product ions.

“…"Fast-" and "slow"-exchanging b fragment structures have been distinguished in this way by a number of groups [18][19][20][21][22][23]. Quantification of "fast" versus "slow" structures can be performed by an analysis of the kinetic rates.…”

Section: Introductionmentioning

confidence: 99%

Disfavoring Macrocycle b Fragments by Constraining Torsional Freedom: The “Twisted” Case of QWFGLM b₆

Tirado

Rutters

Chen

et al. 2012

While recent studies have shown that for some peptides, such as oligoglycines and Leu-enkephalin, mid-sized b fragment ions exist as a mixture of oxazolone and macrocycle structures, other primary structure motifs, such as QWFGLM, are shown to exclusively give rise to macrocycle structures. The aim of this study was to determine if certain amino acid residues are capable of suppressing macrocycle formation in the corresponding b fragment. The residues proline and 4-aminomethylbenzoic acid (4AMBz) were chosen because of their intrinsic rigidity, in the expectation that limited torsional flexibility may impede "head-to-tail" macrocycle formation. The presence of oxazolone versus macrocycle b 6 fragment structures was validated by infrared multiple photon dissociation (IRMPD) spectroscopy, using the free electron laser FELIX. It is confirmed that proline disfavors macrocycle formation in the cases of QPWFGLM b 7 and in QPFGLM b 6 . The 4AMBz substitution experiments show that merely QWFG(4AMBz)M b 6 , with 4AMBz in the fifth position, exhibits a weak oxazolone band. This effect is likely ascribed to a stabilization of the oxazolone structure, due to an extended oxazolone ring-phenyl π-electron system, not due to the rigidity of the 4AMBz residue. These results show that some primary structures have an intrinsic propensity to form macrocycle structures, which is difficult to disrupt, even using residues with limited torsional flexibility.