Discovery and Qualification of Candidate Urinary Biomarkers of Disease Activity in Lupus Nephritis.

Lupus nephritis (LN) is a severe clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Assessment of severity and activity of renal involvement in SLE requires a kidney biopsy, an invasive procedure with limited prognostic value. Noninvasive biomarkers are needed to inform treatment decisions and to monitor disease activity. Proteinuria is associated with disease progression in LN; however, the composition of the LN urinary proteome remains incompletely characterized. To address this, we profiled LN urine samples using complementary mass spectrometry-based methods:  protein gel fractionation, chemical labeling using tandem mass tags, and data-independent acquisition. Combining results from these approaches yielded quantitative information on 2573 unique proteins in urine from LN patients. A multiple-reaction monitoring (MRM) method was established to confirm eight proteins in an independent cohort of LN patients, and seven proteins (transferrin, α-2-macroglobulin, haptoglobin, afamin, α-1-antitrypsin, vimentin, and ceruloplasmin) were confirmed to be elevated in LN urine compared to healthy controls. In this study, we demonstrate that deep mass spectrometry profiling of a small number of patient samples can identify high-quality biomarkers that replicate in an independent LN disease cohort. These biomarkers are being used to inform clinical biomarker strategies to support longitudinal and interventional studies focused on evaluating disease progression and treatment efficacy of novel LN therapeutics.

Separation and mass spectrometry in microbial metabolomics.

Measurements of low molecular weight metabolites have been increasingly incorporated in the characterization of cellular physiology, qualitative studies in functional genomics, and stress response determination. The application of cutting edge analytical technologies to the measurement of metabolites and the changes in metabolite concentrations under defined conditions have helped illuminate the effects of perturbations in pathways of interest, such as the tricarboxylic acid cycle, as well as unbiased characterizations of microbial stress responses as a whole. Owing to the complexity of microbial metabolite extracts and the large number of metabolites therein, advanced and high-throughput separation techniques in gas chromatography, liquid chromatography, and capillary electrophoresis have been coupled to mass spectrometry - usually high-resolution mass spectrometry, but not exclusively - to make these measurements.

Backbone cleavages and sequential loss of carbon monoxide and ammonia from protonated AGG: a combined tandem mass spectrometry, isotope labeling, and theoretical study.

The fragmentation characteristics of protonated alanylglycylglycine, [AGG + H](+), were investigated by tandem mass spectrometry in MALDI-TOF/TOF, ion trap, and hybrid sector instruments. b(2) is the most abundant fragment ion in MALDI-TOF/TOF, ion trap, and hybrid sector metastable ion (MI) experiments, while y(2) is slightly more abundant than b(2) in collision activated dissociation (CAD) performed in the sector instrument. The A-G amide bond is cleaved on the a(1)-y(2) pathway resulting in a proton-bound dimer of GG and MeCH=NH. Depending on the fragmentation conditions employed, this dimer can then (1) be detected as [AGG + H - CO](+), (2) dissociate to produce y(2) ions, [GG + H](+), (3) dissociate to produce a(1) ions, [MeCH=NH + H](+), or (4) rearrange to expel NH(3) forming a [AGG + H - CO - NH(3)](+) ion. The activation method and the experimental timescale employed largely dictate which of, and to what extent, these processes occur. These effects are qualitatively rationalized with the help of quantum chemical and RRKM calculations. Two mechanisms for formation of the [AGG + H - CO - NH(3)](+) ion were evaluated through nitrogen-15 labeling experiments and quantum chemical calculations. A mechanism involving intermolecular nucleophilic attack and association of the GG and imine fragments followed by ammonia loss was found to be more energetically favorable than expulsion of ammonia in an S(N)2-type reaction.

Formation of water-soluble pincer silver(I)-carbene complexes: a novel antimicrobial agent.

Silver(I)-2,6-bis(ethanolimidazolemethyl)pyridine hydroxide (4a) and silver(I)-2,6-bis(propanolimidazolemethyl)pyridine hydroxide (4b) are water-soluble silver(I)-carbene complexes that were synthesized in high yield by reacting silver(I) oxide with N-substituted pincer ligands 3 (a = 2,6-bis(ethanolimidazoliummethyl)pyridine diiodide, b = 2,6-bis(propanolimidazoliummethylpyridine)pyridine dibromide). The X-ray crystal structure of 4a is a one-dimensional linear polymer, whereas the mass spectroscopy confirms a monomer in the gas phase. A change in the anion of 4a from a hydroxide to a hexafluorophosphate formed a silver(I)-carbene complex 4c that is dimeric in structure and insoluble in water. The bactericidal activities of the water-soluble silver(I)-carbene complexes were found to be improved over that of silver nitrate.

Intramolecular condensation reactions in protonated dipeptides: carbon monoxide, water, and ammonia losses in competition.

The elimination of carbon monoxide and water from a series of protonated dipeptides, [XxxYyy + H](+), is investigated by tandem mass spectrometry experiments and density functional theory. The combined results show that CO loss occurs on the a(1)-y(1) pathway, which begins by rearrangement of the added proton to the amide N-atom and creates the proton-bound dimer of an amino acid (Yyy) and an imine (that from Xxx residue). The loss of H(2)O is initiated from a tautomer in which the added proton has migrated to the hydroxyl group of the C-terminus, thereby promoting the formation of an ion with protonated oxazolone structure (a nominal b(2) ion). The highest yields of [XxxYyy + H - CO](+) and [XxxYyy + H - H(2)O](+) are observed at threshold energies. As the internal energy of the protonated dipeptides increases, these primary products are depleted by consecutive dissociations yielding mostly backbone fragments. Specifically, [XxxYyy + H - CO](+) decomposes to y(1) (protonated Yyy) and a(1) (immonium ion of Xxx residue), while [XxxYyy + H - H(2)O](+) produces a(2) and the immonium ions of residues Xxx (a(1)) and Yyy ("internal" immonium ion). Water loss takes place more efficiently when the more basic residue is at the C-terminal position. Increasing the basicity of the N-terminal residue enhances the extent of CO versus H(2)O loss and introduces the competitive elimination of NH(3). The dissociations leading to eliminations of small neutrals (CO, H(2)O, etc.) generally proceed over transition states that lie higher in energy than the corresponding dissociation products. The excess energy is disposed of either in translational or rovibrational modes of the products, depending on the stability of the incipient noncovalent assemblies emerging during the cleavage of the small neutrals.

Analysis of amino acid isotopomers using FT-ICR MS.

Fluxes through known metabolic pathways and the presence of novel metabolic reactions are often determined by feeding isotopically labeled substrate to an organism and then determining the isotopomer distribution in amino acids in proteins. However, commonly used techniques to measure the isotopomer distributions require derivatization prior to analysis (gas chromatography/mass spectrometry (GC/MS)) or large sample sizes (nuclear magnetic resonance (NMR) spectroscopy). Here, we demonstrate the use of Fourier transform-ion cyclotron resonance mass spectrometry with direct infusion via electrospray ionization to rapidly measure the amino acid isotopomer distribution in a biomass hydrolysate of the soil bacterium Desulfovibrio vulgaris Hildenborough. By applying high front-end resolution for the precursor ion selection followed by sustained off-resonance irradiation collision-induced dissociation, it was possible to determine exactly and unambiguously the specific locations of the labeled atoms in the amino acids, which usually requires a combination of 2-D 13C NMR spectroscopy and GC/MS. This method should be generally applicable to all biomass samples and will allow more accurate determination of metabolic fluxes with less work and less sample.

Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry.

Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.

Characterization of dipeptide isomers by tandem mass spectrometry of their mono- versus dilithiated complexes.

The Li+ complexes of the isomeric dipeptide pairs PheGly/GlyPhe, PheAla/AlaPhe, and TrpAla/AlaTrp, namely, [Pep + Li]+, and of the corresponding lithium carboxylates, namely, [Pep - H + 2Li]+, are produced in the gas phase by desorption ionization, and their unimolecular chemistry is probed by tandem mass spectrometry experiments at various activation conditions. At low internal energies, monolithiated isomers dissociate to the same products, formed through a mixed anhydride intermediate in which the sequence information is lost. Isomerization to the mixed anhydride is less competitive at higher internal energies, which start promoting sequence-specific fragmentations. On the other hand, dilithiated isomers (they contain a permanent COO-Li+ salt bridge) do not rearrange to an anhydride and give rise to substantially different fragmentation patterns; structurally diagnostic c1- and y1-type fragments are observed at all internal energies, allowing for unequivocal sequence assignment. The mono- and dilithiated peptides undergo loss of their aromatic side chain to form distonic radical ions carrying Li+ charge(s) and one unpaired electron at an alpha-C atom of the peptide backbone. The yield of such metal-bound peptide radicals is particularly high from the dilithiated complexes, [Pep - H + 2Li]+. Upon activation, the Li+ ions become mobile and can be shuttled to the various basic sites of the dipeptides, where they may initiate backbone fragmentation or the elimination of small neutral molecules.