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

Identification of process related trace level impurities in the actinide decorporation agent 3,4,3-LI(1,2-HOPO): Nozzle-skimmer fragmentation via ESI LC-QTOFMS

3,4,3-LI(1,2-HOPO) is a chelating ligand and decorporation agent that can remove radioactive lanthanides and actinides from the body. Identification of trace impurities in drug samples is gaining much interest due to their significant influence on drug activity. In this study, trace impurities were detected in manufactured lots of 3,4,3-LI(1,2-HOPO) by a developed method of liquid chromatography coupled with photo-diode array UV detection and electrospray ionization-quadrupole time of flight mass spectrometry (LC-QTOFMS), via induced-in-source or collision-induced mass fragmentation (nozzle-skimmer fragmentation). Molecular ions were fragmented within the nozzle-skimmer region of electrospray ionization (ESI) mass spectrometer equipped with a Time of Flight detector. Eight major (detected at levels higher than a 0.1% threshold) and seven minor trace impurities were identified. The respective structures of these impurities were elucidated via analysis of the generated fragment ions using mass fragmentation and elemental composition software. Proposed structures of impurities were further confirmed via isotopic modeling.

Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment

The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%.

Two-dimensional ECD FT-ICR mass spectrometry of peptides and glycopeptides

2D FT-ICR MS allows the correlation between precursor and fragment ions by modulating ion cyclotron radii for fragmentation modes with radius-dependent efficiency in the ICR cell without the need for prior ion isolation. This technique has been successfully applied to ion-molecule reactions, Collision-induced dissociation and infrared multiphoton dissociation. In this study, we used electron capture dissociation for 2D FT-ICR MS for the first time, and we recorded two-dimensional mass spectra of peptides and a mixture of glycopeptides that showed fragments that are characteristic of ECD for each of the precursor ions in the sample. We compare the sequence coverage obtained with 2D ECD FT-ICR MS with the sequence coverage obtained with ECD MS/MS and compare the sensitivities of both techniques. We demonstrate how 2D ECD FT-ICR MS can be implemented to identify peptides and glycopeptides for proteomics analysis.

Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions

Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule-receptor interactions, this technique has also been applied to study protein-protein complexes, such as mapping antibody-antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery.

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.

Speciation of nitrogen containing aromatics by atmospheric pressure photoionization or electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

We determine the elemental compositions of aromatic nitrogen model compounds as well as a petroleum sample by atmospheric pressure photoionization (APPI) and electrospray Ionization (ESI) with a 9.4 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. From the double-bond equivalents calculated for the nitrogen-containing ions from a petroleum sample, we can infer the aromatic core structure (pyridinic versus pyrrolic nitrogen heterocycle) based on the presence of M(+.) (odd-electron) versus [M+H](+) (even-electron) ions. Specifically, nitrogen speciation can be determined from either a single positive-ion APPI spectrum or two ESI (positive- and negative-ion) spectra. APPI operates at comparatively higher temperature than ESI and also produces radical cations that may fragment before detection. However, APPI fragmentation of aromatics can be eliminated by judicious choice of instrumental parameters.

Distortion of ion structures by field asymmetric waveform ion mobility spectrometry

Field asymmetric waveform ion mobility spectrometry (FAIMS) is emerging as a major analytical tool, especially in conjunction with mass spectrometry (MS), conventional ion mobility spectrometry (IMS), or both. In particular, FAIMS is used to separate protein or peptide conformers prior to characterization by IMS, MS/MS, or H/D exchange. High electric fields in FAIMS induce ion heating, previously estimated at <10 degrees C on average and believed too weak to affect ion geometries. Here we use a FAIMS/IMS/MS system to compare the IMS spectra for ESI-generated ubiquitin ions that have and have not passed FAIMS and find that some unfolding occurs for most charge states. These data and their comparison with the reported protein unfolding in a Paul trap imply that at least some structural transitions observed in FAIMS, or previously in an ion trap, are not spontaneous. The observed unfolding is similar to that produced by heating of approximately 50 degrees C above room temperature, consistent with the calculated heating of ions at FAIMS waveform peaks. Hence, the ion isomerization in FAIMS likely proceeds in steps during the "hot" periods, especially right after entering the device. The process distorts ion geometries and causes ion losses by a "self-cleaning" mechanism and thus should be suppressed as much as possible. We propose achieving that via cooling FAIMS by the amount of ion heating; in most cases, cooling by approximately 75 degrees C should suffice.