Inter-molecular migration during collisional activation monitored by hydrogen/deuterium exchange FT-ICR tandem mass spectrometry

Hydrogen/deuterium exchange mass spectrometry in the world of small molecules

The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.

Gas-Phase Hydrogen/Deuterium Scrambling in Negative-Ion Mode Tandem Mass Spectrometry

Hydrogen/deuterium exchange coupled with mass spectrometry (HDX MS) has become a powerful method to characterize protein conformational dynamics. Workflows typically utilize pepsin digestion prior to MS analysis to yield peptide level structural resolution. Tandem mass spectrometry (MS/MS) can potentially facilitate determination of site-specific deuteration to single-residue resolution. However, to be effective, MS/MS activation must minimize the occurrence of gas-phase intramolecular randomization of solution-generated deuterium labels. While significant work has focused on understanding this process in positive-ion mode, little is known about hydrogen/deuterium (H/D) scrambling processes in negative-ion mode. Here, we utilize selectively deuterated model peptides to investigate the extent of intramolecular H/D scrambling upon several negative-ion mode MS/MS techniques, including negative-ion collision-induced dissociation (nCID), electron detachment dissociation (EDD), negative-ion free radical-initiated peptide sequencing (nFRIPS), and negative-ion electron capture dissociation (niECD). H/D scrambling was extensive in deprotonated peptides upon nCID and nFRIPS. In fact, the energetics required to induce dissociation in nCID are sufficient to allow histidine C-2 and C_β hydrogen atoms to participate in the scrambling process. EDD and niECD demonstrated moderate H/D scrambling with niECD being superior in terms of minimizing hydrogen migration, achieving ~ 30% scrambling levels for small c-type fragment ions. We believe the observed scrambling is likely due to activation during ionization and ion transport rather than during the niECD event itself.

Hydrogen/deuterium exchange in mass spectrometry

The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

CID fragmentation, H/D exchange and supermetallization of Barnase-Barstar complex

The barnase-barstar complex is one of the most stable protein-protein complexes and has a very wide range of possible applications. Here we report the use of top-down mass spectrometry for the investigation of the structure of this complex, its ionization via ESI, isolation and fragmentation. It was found that the asymmetry of the resulting charge state distributions of the protein monomer product ions increased as the charge state of the precursor ions increased. For the investigation of the 3D structure of the complex, the gas phase H/D exchange reaction was used. In addition, supermetallized ions of the complex with Zn were produced and investigated. It was observed that an increase in the number of metals bound to the complex results in a change in complex stability and the charge distribution between protein fragment. Analysis of the fragmentation pattern of the supermetallized complex [bn-b* + 5Zn]¹⁰⁺ indicated that this ion is present in different conformations with different charges and Zn distributions. Since Zn cannot migrate, such structures must be formed during ionization.

Nonuniform isotope patterns produced by collision-induced dissociation of homogeneously labeled ubiquitin: implications for spatially resolved hydrogen/deuterium exchange ESI-MS studies

There is an ongoing debate whether collision-induced dissociation (CID) of electrosprayed proteins after solution-phase hydrogen/deuterium exchange (HDX) is a viable approach for determining spatially resolved deuteration patterns. This work explores the use of two methods, source-CID and hexapole tandem mass spectrometry (MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer, for measuring the fragment deuteration levels of regioselectively labeled ubiquitin. Both methods reveal that b-ions exhibit HDX levels significantly below that of the intact protein, whereas several y'' fragments are labeled to a much greater extent. These results are consistent with earlier source-CID data (Akashi, S.; Naito, Y.; Takio, K. Anal. Chem. 1999, 71, 4974-4980). However, the measured b-ion deuteration levels are in disagreement with the known solution-phase behavior of ubiquitin. Partial agreement is observed for y''-ions. Control experiments on homogeneously labeled ubiquitin (having the same average deuteration level at every exchangeable site) result in highly nonuniform fragment HDX levels. In particular, b-ions exhibit deuteration levels significantly below that of intact ubiquitin, thereby mimicking the behavior seen for the regioselectively labeled protein. This effect is likely caused by isotope fractionation during collisional activation, facilitated by the high mobility of charge carriers (scrambling) in the gas phase. The observation that the b-ion labeling behavior is largely independent of the spatial isotope distribution within solution-phase ubiquitin invalidates these ions as reporters of the protein deuteration pattern. This work questions the common practice of interpreting any nonuniformities in fragment deuteration as being indicative of regioselective solution-phase labeling. Artifactual deuterium enrichment or depletion during collisional activation may have contributed to the current lack of consensus as to whether HDX/CID represents a potentially viable tool for measuring solution-phase deuteration patterns.

Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction

To explore the mechanism of electron capture dissociation (ECD) of linear peptides, a set of 16-mer peptides were synthesized with deuterium labeled on the alpha-carbon position of four glycines. The ECD spectra of these peptides showed that such peptides exhibit a preference for the radical to migrate to the alpha-carbon position on glycine via hydrogen (or deuterium) abstraction before the final cleavage and generation of the detected product ions. The data show c-type fragment ions, ions corresponding to the radical cation of the c-type fragments, c*, and they also show c*-1 peaks in the deuterated peptides only. The presence of the c*-1 peaks is best explained by radical-mediated scrambling of the deuterium atoms in the long-lived, metastable, radical intermediate complex formed by initial electron capture, followed by dissociation of the complex. These data suggest the presence of at least two mechanisms, one slow, one fast. The abundance of H* and -CO losses from the precursor ion changed upon deuterium labeling indicating the presence of a kinetic isotope effect, which suggests that the values reported here represent an underestimation of radical migration and H/D scrambling in the observed fragments.

Solution-phase deuterium/hydrogen exchange at a specific residue using nozzle-skimmer and electron capture dissociation mass spectrometry

Information about protein conformation can be obtained with hydrogen/deuterium exchange (HDX) mass spectrometry. The isotopic solution-phase exchange of specific amide hydrogen atoms can be followed using low-vacuum nozzle-skimmer collision-induced dissociation (CID). In this study, the nozzle-skimmer technique was complemented by electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The solution-phase exchange at a specific residue is monitored by comparing isotopic distributions of two consecutive b- or c-type ions. While nozzle-skimmer fragmentation takes place in the low-vacuum region of the mass spectrometer, ECD occurs at ultra-high vacuum within the mass analyzer cell of the FTICR mass spectrometer. The dissociations take place at 10(-4) and 10(-9) mbar, respectively. Low-vacuum nozzle-skimmer fragmentation can result in intramolecular exchange between product ions and solvent molecules in the gas phase. Consequently, the solution-phase information about protein or peptide conformation is lost. It was not possible to monitor isotopic solution-phase exchange at the eighth residue in substance P, (Phe)8, with nozzle-skimmer CID. By using the in-cell ECD fragmentation method, the solution-phase exchange at the (Phe)8 residue was preserved during mass spectrometric analysis. This result shows the complementary aspects of applying fragmentation at low and at high vacuum, when studying isotopic exchange in solution at specific residues using FTICRMS.

Site-specific amide hydrogen exchange in melittin probed by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry

Electron capture dissociation (ECD) has been proposed to be a non-ergodic process, i.e. to provide backbone dissociation of gas-phase peptides faster than randomization of the imparted energy. One potential consequence could be that ECD can fragment deuterated peptides without causing hydrogen scrambling and thereby provide amino acid residue-specific amide hydrogen exchange rates. Such a feature would improve the resolution of approaches involving solution-phase amide hydrogen exchange combined with mass spectrometry for protein structural characterization. Here, we explore this hypothesis using melittin, a haemolytic polypeptide from bee venom, as our model system. Exchange rates in methanol calculated from consecutive c-type ion pairs show some correlation with previous NMR data: the amide hydrogens of leucine 13 and alanine 15, located at the unstructured kink surrounding proline 14 in the melittin structure adopted in methanol, appear as fast exchangers and the amide hydrogens of leucine 16 and lysine 23, buried within the helical regions of melittin, appear as slow exchangers. However, calculations based on c-type ions for other amide hydrogens do not correlate well with NMR data, and evidence for deuterium scrambling in ECD was obtained from z*-type ions.

Intramolecular Migration of Amide Hydrogens in Protonated Peptides upon Collisional Activation

Presently different opinions exist as to the degree of scrambling of amide hydrogens in gaseous protonated peptides and proteins upon collisional activation in tandem mass spectrometry experiments. This unsettled controversy is not trivial, since only a very low degree of scrambling is tolerable if collision-induced dissociation (CID) should provide reliable site-specific information from (1)H/(2)H exchange experiments. We have explored a series of unique, regioselectively deuterium-labeled peptides as model systems to probe for intramolecular amide hydrogen migration under low-energy collisional activation in an orthogonal quadrupole time-of-flight electrospray ionization (Q-TOF ESI) mass spectrometer. These peptides contain a C-terminal receptor-binding sequence and an N-terminal nonbinding region. When the peptides form a receptor complex, the amide hydrogens of the interacting sequences are protected against exchange with the solvent, while the amide hydrogens of the nonbinding sequences exchange rapidly with the solvent. We have utilized such long-lived complexes to generate peptides labeled with deuterium in either the binding or nonbinding region, and the expected regioselectivity of this labeling was confirmed after pepsin proteolysis. CID of such deuterated peptides, [M + 2H](2+), yielded fragment ions (b- and y-ions) having a deuterium content that resemble the theoretical values calculated for 100% scrambling. Thus, complete randomization of all hydrogen atoms attached to nitrogen and oxygen occurs in the gaseous peptide ion prior to its dissociation.

Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry

Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.