Fragmentation mechanisms of oxidized peptides elucidated by SID, RRKM modeling, and molecular dynamics

The gas-phase fragmentation reactions of singly charged angiotensin II (AngII, DR⁺VYIHPF) and the ozonolysis products AngII+O (DR⁺VY*IHPF), AngII+3O (DR⁺VYIH*PF), and AngII+4O (DR⁺VY*IH*PF) were studied using SID FT-ICR mass spectrometry, RRKM modeling, and molecular dynamics. Oxidation of Tyr (AngII+O) leads to a low-energy charge-remote selective fragmentation channel resulting in the b ₄ +O fragment ion. Modification of His (AngII+3O and AngII+4O) leads to a series of new selective dissociation channels. For AngII+3O and AngII+4O, the formation of [MH+3O] ⁺ −45 and [MH+3O] ⁺ −71 are driven by charge-remote processes while it is suggested that b ₅ and [MH+3O] ⁺ −88 fragments are a result of charge-directed reactions. Energy-resolved SID experiments and RRKM modeling provide threshold energies and activation entropies for the lowest energy fragmentation channel for each of the parent ions. Fragmentation of the ozonolysis products was found to be controlled by entropic effects. Mechanisms are proposed for each of the new dissociation pathways based on the energies and entropies of activation and parent ion conformations sampled using molecular dynamics.     

Eliminating false positive C4 sugar tests on New Zealand Manuka honey

Carbon isotope analyses (δ¹³C) of some New Zealand Manuka honeys show that they often fail the internationally recognised Association of Official Analytical Chemists sugar test (AOAC method 998.12) which detects added C₄ sugar, although these honeys are from unadulterated sources. Failure of these high value products is detrimental to the New Zealand honey industry, not only in lost export revenue, but also in brand and market reputation damage. The standard AOAC test compares the carbon isotope value of the whole honey and corresponding protein isolated from the same honey. Differences between whole honey and protein δ¹³C values should not be greater than +1.0‰, as it indicates the possibility of adulteration with syrups or sugars from C₄ plants such as high fructose corn syrup or cane sugar. We have determined that during the standard AOAC method, pollen and other insoluble components are isolated with the flocculated protein. These non‐protein components have isotope values which are considerably different from those of the pure protein, and can shift the apparent δ¹³C value of protein further away from the δ¹³C value of the whole honey, giving a false positive result for added C₄ sugar. To eliminate a false positive C₄ sugar test for Manuka honey, prior removal of pollen and other insoluble material from the honey is necessary to ensure that only the pure protein is isolated. This will enable a true comparison between whole honey and protein δ¹³C isotopes. Furthermore, we strongly suggest this modification to the AOAC method be universally adopted for all honey C₄ sugar tests. Copyright © 2010 John Wiley & Sons, Ltd.     

Study of bisphosphonates by matrix‐assisted laser desorption/ionization mass spectrometry – influence of alkali atoms on fragmentation patterns

1‐Hydroxymethylene‐1,1‐bisphosphonic acids (or bisphosphonates) are compounds that have interesting pharmacological applications. However, few mass spectrometric investigations have been carried out to determine their fragmentation patterns. Herein, we evaluated different matrices for the study by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) of the formation and fragmentation of the protonated, the cationized (MNa⁺ and MK⁺) and the deprotonated bisphosphonates. Some in‐source fragmentations were observed both in positive and in negative ion modes. The fragmentation patterns obtained in post‐source decay mode are also discussed. In contrast to previous electrospray ionization/multi‐stage mass spectrometry (ESI‐MSⁿ) studies, some new fragmentation pathways were deduced and the effects of alkali ions on the fragmentation patterns were shown. The results summarized here completed the data previously recorded by ESI‐MSⁿ and could be used for the characterization of bisphosphonates as alkali complexes in biological mixtures. Copyright © 2009 John Wiley & Sons, Ltd.     

Use of ion mobility mass spectrometry and a collision cross‐section algorithm to study an organometallic ruthenium anticancer complex and its adducts with a DNA oligonucleotide

We report the development of an enhanced algorithm for the calculation of collision cross‐sections in combination with Travelling‐Wave ion mobility mass spectrometry technology and its optimisation and evaluation through the analysis of an organoruthenium anticancer complex [(η⁶‐biphenyl)Ru^II(en)Cl]⁺. Excellent agreement was obtained between the experimentally determined and theoretically determined collision cross‐sections of the complex and its major product ion formed via collision‐induced dissociation. Collision cross‐sections were also experimentally determined for adducts of this ruthenium complex with the single‐stranded oligonucleotide hexamer d(CACGTG). Ion mobility tandem mass spectrometry measurements have allowed the binding sites for ruthenium on the oligonucleotide to be determined. Copyright © 2009 John Wiley & Sons, Ltd.     

High‐field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high‐resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides

We have applied high‐field asymmetric waveform ion mobility spectrometry (FAIMS) to the analysis of the phosphopeptides APLpSFRGSLPKSYVK, APLSFRGpSLPKSYVK, and APLSFRGSLPKpSYVK. The peptides have identical amino acid sequences and differ only in the site of phosphorylation. The results show that FAIMS is capable of at least partially separating these species. Separation was confirmed by coupling FAIMS with high‐resolution electron transfer dissociation (ETD) mass spectrometry. Phosphorylation is retained on the ETD peptide fragments thereby allowing assignment of the site of the modification. Co‐eluting phosphopeptides which differ only in the site of modification are frequently observed in liquid chromatography/tandem mass spectrometry phosphoproteomics experiments, and therefore these proof‐of‐principle results have implications for the application of FAIMS in that field. Copyright © 2009 John Wiley & Sons, Ltd.     

Automated Spleen Injury Detection Using 3D Active Contours and Machine Learning

The spleen is one of the most frequently injured organs in blunt abdominal trauma. Computed tomography (CT) is the imaging modality of choice to assess patients with blunt spleen trauma, which may include lacerations, subcapsular or parenchymal hematomas, active hemorrhage, and vascular injuries. While computer-assisted diagnosis systems exist for other conditions assessed using CT scans, the current method to detect spleen injuries involves the manual review of scans by radiologists, which is a time-consuming and repetitive process. In this study, we propose an automated spleen injury detection method using machine learning. CT scans from patients experiencing traumatic injuries were collected from Michigan Medicine and the Crash Injury Research Engineering Network (CIREN) dataset. Ninety-nine scans of healthy and lacerated spleens were split into disjoint training and test sets, with random forest (RF), naive Bayes, SVM, k-nearest neighbors (k-NN) ensemble, and subspace discriminant ensemble models trained via 5-fold cross validation. Of these models, random forest performed the best, achieving an Area Under the receiver operating characteristic Curve (AUC) of 0.91 and an F1 score of 0.80 on the test set. These results suggest that an automated, quantitative assessment of traumatic spleen injury has the potential to enable faster triage and improve patient outcomes.     

Importance of palladium-carbon bond energies in direct arylation of polyfluorinated benzenes

Fagnou et al. reported direct arylation reactions that use palladium catalysts to couple Ar(1)-X to Ar(2)-H with the aid of a coordinated base. These reactions are particularly favourable for polyfluorinated arenes Ar(2)-H (see S. I. Gorelsky, D. Lapointe and K. Fagnou, J. Am. Chem. Soc. 2008, 130, 10848). In this paper, we show by means of a DFT analysis how the energetics and activation energies vary with fluorine substitution and examine the structures of intermediates and transition states. The reactant is modelled by Pd(OAc)(Ph)(PMe(3))(DMA) (DMA = dimethylacetamide). The sequence consists of (a) replacement of DMA by arene, (b) Concerted Deprotonation Metallation (CMD), (c) decoordination of AcOH, (d) reductive elimination of biaryl. Many of the variations are dominated by the number of fluorine substituents ortho to the C-H bond and fall into three groups labelled accordingly: Set0Fo, Set1Fo, and Set2Fo. In the first step a coordinated solvent is replaced by the arene. The arenes of Set0Fo and Set1Fo coordinate in a conventional η(2)-CH=CH mode, whereas the arenes of Set2Fo coordinate in an η(1)-CH mode assisted by an OH-C hydrogen bond from the coordinated acetate. Both the energy barriers to CMD and the product energies fall into the three typical sets with the highest barrier and highest product energy being for Set0Fo. They correlate more satisfactorily with the variations in Pd-C bond energies than with the C-H acidities. The barriers to reductive elimination from Pd(Ph)(Ar(F))(PMe(3))(AcOH) increase systematically from Set0Fo to Set2Fo as the Pd-C bond becomes stronger in a regular fashion from Set0Fo to Set2Fo. Again there is a strong correlation between the energy barriers to reductive elimination and the Pd-C bond energies. It is found overall that the key aspects of the reactions are: (a) the lowering of the energy of the CMD step by the ortho fluorine substituents, (b) the regioselective activation of C-H bonds ortho to fluorine which is also determined at the CMD step, (c) the decoordination of AcOH, which maintains the transition state for reductive elimination at low Gibbs free energy. The presence of fluorine increases the effectiveness of the reaction in the sense of points a and b via the increasing strength of the palladium-carbon bond.     

Tripyrrolidinophosphoric acid triamide as an activator in samarium diiodide reductions

The electrochemical and spectrophotometric characterization of the complex formed from samarium diiodide and 4 equiv of tripyrrolidinophosphoric acid triamide (TPPA) is presented. Kinetic studies indicate that the SmI(2)/TPPA complex possesses reactivity greater than the complex formed between samarium diiodide and 4 equiv of HMPA. Examples of the use of SmI(2)/TPPA in synthesis are presented.