A recommended and verified procedure for in situ tryptic digestion of formalin‐fixed paraffin‐embedded tissues for analysis by matrix‐assisted laser desorption/ionization imaging mass spectrometry

Matrix‐assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin‐fixed paraffin‐embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross‐links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.     

Heterotrimetallic Mixed-Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

A known trinuclear structure was used to design the heterobimetallic mixed-valent, mixed-ligand molecule [Co^II(hfac)₃−Na−Co^III(acac)₃] ( 1 ). This was used as a template structure to develop heterotrimetallic molecules [Co^II(hfac)₃−Na−Fe^III(acac)₃] ( 2 ) and [Ni^II(hfac)₃−Na−Co^III(acac)₃] ( 3 ) via isovalent site-specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple-wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di- and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O₄ functional oxide materials.     

The influence of amine/amide versus bisamide coordination in nickel superoxide dismutase

Nickel superoxide dismutase (NiSOD) is a mononuclear nickel-containing metalloenzyme that catalyzes the disproportionation of superoxide by cycling between NiII and NiIII oxidation states. In the reduced NiII oxidation state, the metal center is ligated by two cysteinate sulfurs, one amide nitrogen, and one amine nitrogen (from the N-terminus), while in the oxidized NiIII state, an imidazole nitrogen coordinates to the metal center. Herein, we expand on a previous report in which we described a functional metallopeptide-based NiSOD model compound [NiII(SODM1)] (SODM1 = H2N-HCDLPCGVYDPA-COOH) by exploring how acylation of the N-terminus (producing [NiII(SODM1-Ac)]) influences the properties of the metallopeptide. Titration results, GPC data, and mass-spectrometry data demonstrate that NiII coordinates to SODM1-Ac in a 1:1 ratio, while variable pH studies show that NiII coordination is strong at a pH of 7.5 and above but not observed below a pH of 6.2. This is higher than [NiII(SODM1)] by approximately 1.0 pH unit consistent with bisamide ligation. Ni K-edge XAS demonstrates that the NiII center is coordinated in a square-planar NiN2S2 coordination environment with Ni-N distances of 1.846(4) A and Ni-S distances of 2.174(3) A. Comparison of the electronic absorption and CD spectrum of [NiII(SODM1)] versus [NiII(SODM1-Ac)] in conjunction with time-dependent DFT calculations suggests a decrease in Ni covalency in the acylated versus unacylated metallopeptide. This decrease in covalency was also supported by DFT calculations and Ni L-edge XAS. [NiII(SODM1-Ac)] has a quasireversible NiII/NiIII redox couple of 0.49(1) V vs Ag/AgCl, which represents a -0.2 V shift compared with [NiII(SODM1)], while the peak separation suggests a change in the coordination environment upon oxidation (i.e., axial imidazole ligation). Using the xanthine/xanthine oxidase assay, we determine that [NiII(SODM1-Ac)] is less active than [NiII(SODM1)] by over 2 orders of magnitude (IC50 = 3(1) x 10-5 vs 2(1) x 10-7 M). Possible reasons for the decrease in activity are discussed.     

A Facile Synthesis and Crystallographic Analysis of Seven Trityl Phosphorus Compounds and Two Nickel(II) Phosphine Side-Products

Abstract  The syntheses and X-ray analyses of triphenylmethyl (trityl=Tr) phosphorus compounds are reported and the structural similarities, differences and ³¹P chemical shifts compared. A series of seven trityl-substituted phosphorus-containing compounds have been characterized by single crystal X-ray diffraction. Ph₃CPPh₂, 1, a bulky P(III) compound crystallizes in the triclinic space group , a = 7.5624(6) ?, b = 9.5470(8) ?, c = 16.9722(14) ?, α = 83.4720(10)°, β = 80.541(2)°, γ = 68.1580(10)°, the borane complex of 1, 2, Ph₃CPPh₂(BH₃) crystallizes as monoclinic colorless crystals, P2₁/c, a = 10.0972(12) ?, b = 9.6955(12) ?, c = 25.197(3) ?, β = 90.258(2)°. The analogous methyl substituted, 3, Ph₃CPMe₂(BH₃) is monoclinic, C₂/c, a = 15.628(3) ?, b = 12.770(3) ?, c = 18.406(4) ?, β = 103.968(3)°. Compounds 4–7 are trityl substituted P(V) compounds: Ph₃CP(Ph)(O)(OH), 4, crystallizes in the triclinic space group , a = 8.9847(18) ?, b = 9.7443(19) ?, c = 12.786(3) ?, α = 72.045(3)°, β = 72.031(3)°, γ = 78.769(3)°. Esterification of 4 affords TrCP(O)(Ph)OBn 5, space group, P2₁/c, a = 7.9196(5) ?, b = 31.701(2) ?, c = 19.8062(13) ?, β = 99.7750(10)°. A phosphonate diester was also characterized, Ph₃CP(O)(OEt)₂, 6, triclinic, , a = 7.9521(17) ?, b = 9.2205(19) ?, c = 14.471(3) ?, α = 85.906(4)°, β = 83.031(4)°, γ = 68.283(4)°. Treatment of the trityl H-phosphinic acid, Ph₃CPO₂H_2, with elemental selenium yields yellow crystals of 7, [Ph₃CP(O)(OH)Se]_2, P2₁/c, a = 9.0603(4) ?, b = 22.3652(11) ?, c = 16.9134(7) ?, β = 107.035(2)°. In our efforts to isolate a nickel-phosphine complex, two Ni(II) complexes were crystallographically analyzed, [Ni(OP(H)Ph₂)₆]₂BF₄ ⁻ 8 and 9. Complex 8 with an uncoordinated BF₄ ⁻ ion crystallizes as yellow orthorhombic crystals, Pbca, a = 18.8247(12) ?, b = 18.5518(12) ?, c = 21.0976(14) ?, while crystals of 9 are trigonal, , a = b = 13.1545(12) ?, c = 68.461(9) ?. Graphical Abstract  The syntheses and X-ray analyses of triphenylmethyl (trityl=Tr) phosphorus compounds are reported and the structural similarities, differences and ³¹P chemical shifts compared.      

LC–MS Method for the Pharmacokinetic Evaluation of 2-Arachidonoyl Glycerol in Small Volume Plasma Samples

A quantitative method has been developed and validated for the determination of 2-arachidonoylglycerol (2-AG) in hairless guinea pig plasma by liquid chromatographic-electrospray ionization mass spectrometry. The analytes were extracted from the plasma samples of guinea pig by a single step liquid extraction technique using acetonitrile. The chromatographic separation was conducted on a C18 column using a gradient mobile phase consisting of methanol and water at a flow rate of 0.3 mL min^?1. The analytes were quantified by positive electrospray ionization mass spectrometry with selected ion monitoring mode of m/z 401. The limit of detection for 2-AG was 0.5 ng mL^?1. This method required only simple processing of the samples to prevent the isomerization of 2-AG during sampling and handling and could be applied to determine the plasma concentration profiles in hairless guinea pigs. The volume of distribution at steady state (V _ss), total plasma clearance (CL) and half life (t _1/2β) of 2-AG in hairless guinea pigs were 0.21 ± 0.025 L kg^?1, 9.2 ± 1.5 L h^?1 kg^?1, and 17.7 ± 3.8 min, respectively.     

The synthesis and characterization of germanium dichloride and dimethyl aluminium chloride derivatives of the 2,2-dipyridylamine ligand

The reactions of germanium dichloride and dimethyl aluminium chloride with 2,2-dipyridylamine (dpa) affords germanium and organo-aluminium complexes. Structural characterization reveals that the preferential coordination site of both germanium and aluminium is within the sterically protected pyridyl, (pyridyl = C₅H₅N = py), pocket. Py₂NGeCl, compound (1), crystallizes in the triclinic space group, P-1, with cell coordinates; a=8.2956(11), b=9.9938(13), c=12.6517(17), α=92.033(2)°, β=92.834(2)°, γ=91.685(2)°. The aluminium complex, Py₂NAlMe₂·Al(Me)Cl, (2), crystallizes in the orthorhombic space group, Pna2(1), with cell parameters: a=13.3707(10), b=10.8706(8), c=16.1306(12). The X-ray analysis of the side products of these reactions, the lithium halide adducts are also reported.     

Reactions of β-diketiminates with selenium and tellurium halides

The complexes [nacnacTeCl₄] and nacnacSeCl⁺Cl⁻ (nacnac = [{N(C₆H₃ⁱPr₂2,6)C(Me)}₂CH]⁻) have been prepared in good yields and characterized in the solid state by X-ray crystallography. The crystals of both compounds show C-H activation of the ligand backbone. In the case of tellurium, no LiCl displacement or nitrogen chelation is observed and an ionic TeCl₄ complex is isolated. By contrast, under similar reaction conditions, the reaction with SeCl₄, affords a cationic Se(II) complex with loss of four chlorines and rearrangement of the chloride atom to the nacnac ligand.     

Synthesis of 2-indanones via [4 + 1] annulation reactions of (trialkylsilyl)arylketenes

[reaction: see text] (Trialkylsilyl)arylketenes combine with (trimethylsilyl)diazomethane in a new [4 + 1] annulation process leading to 2-indanone derivatives. The (trialkylsilyl)arylketene annulation substrates are available via the photochemical Wolff rearrangement of alpha-silyl-alpha-diazo ketones, which are themselves prepared by silylation of the corresponding diazo ketones. The mechanism of the annulation reaction is proposed to involve the formation of a 2,3-bis(silyl)cyclopropanone, which is in equilibrium with an oxyallylic cation. Electrocyclic closure of this intermediate forms the new cyclopentenone ring.     

Glycosylation States on Intact Proteins Determined by NMR Spectroscopy

Protein glycosylation is important in many organisms for proper protein folding, signaling, cell adhesion, protein-protein interactions, and immune responses. Thus, effectively determining the extent of glycosylation in glycoprotein therapeutics is crucial. Up to now, characterizing protein glycosylation has been carried out mostly by liquid chromatography mass spectrometry (LC-MS), which requires careful sample processing, e.g., glycan removal or protein digestion and glycopeptide enrichment. Herein, we introduce an NMR-based method to better characterize intact glycoproteins in natural abundance. This non-destructive method relies on exploiting differences in nuclear relaxation to suppress the NMR signals of the protein while maintaining glycan signals. Using RNase B Man5 and RNase B Man9, we establish reference spectra that can be used to determine the different glycoforms present in heterogeneously glycosylated commercial RNase B.