Distributed computing strategies for processing of FT-ICR MS imaging datasets for continuous mode data visualization

High-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry imaging enables the spatial mapping and identification of biomolecules from complex surfaces. The need for long time-domain transients, and thus large raw file sizes, results in a large amount of raw data (“big data”) that must be processed efficiently and rapidly. This can be compounded by large-area imaging and/or high spatial resolution imaging. For FT-ICR, data processing and data reduction must not compromise the high mass resolution afforded by the mass spectrometer. The continuous mode “Mosaic Datacube” approach allows high mass resolution visualization (0.001 Da) of mass spectrometry imaging data, but requires additional processing as compared to feature-based processing. We describe the use of distributed computing for processing of FT-ICR MS imaging datasets with generation of continuous mode Mosaic Datacubes for high mass resolution visualization. An eight-fold improvement in processing time is demonstrated using a Dutch nationally available cloud service.

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Determination of unique amino acid substitutions in protein variants by peptide mass mapping with FT-ICR MS

Peptide mass mapping plays a central role in the structural characterization of protein variants with single amino acid substitutions. Among the 20 standard amino acids found in living organisms, 18, all but Leu and Ile, differ from each other in molecular mass. The mass differences between amino acids range from 0.0364 to 129.0578 Da. The mass of the mutated peptide or the difference between normal and mutated peptides uniquely determines the type of substitution in some cases, and even pinpoints the position of the mutation when the involved residue is found only once in the peptide. Among 75 pairs of amino acid residues that are exchangeable via a single nucleotide replacement, 53 show specific change in exact mass, while only 25 in nominal mass. On the other hand, precise measurement, at least to the third decimal place, greatly enhances the capacity of the peptide mass mapping strategy for structural characterization. This notion was verified by an analysis of three Hb variants using MALDI-FTICR MS. In addition, the baseline resolution of two 1 kDa peptides with a single amino acid difference, Lys or Gln, which have the smallest (0.0364 Da) difference among residues, was achieved by measurement at a mass resolving power of 342,000. The results indicated that the smallest difference, 0.0040 Da between [Delta29.9742 for Glu-Val] and [Delta29.9782 for Trp-Arg], among all types of amino acid substitutions derived from a single nucleotide replacement can be discriminated at the present performance level. Therefore, FTICR MS is capable of identifying all 53 types of substitutions, each of which is associated with a unique mass difference, except for the Leu and Ile isomers.     

An improved potential surface for formaldehyde

A potential energy surface for the ground X? ¹A₁ state of H₂CO has been derived, which reproduces the position of a recently calculated H₂ + CO transition state. The variational method for the determination of frequencies of potential energy surfaces has been extended to tetra-atomics, thus enabling the surface to be refined.     

Target cell extraction coupled with LC‐MS/MS analysis for screening potential bioactive components in Ginkgo biloba extract with preventive effect against diabetic nephropathy

A rapid and useful approach for screening potential bioactive components in Ginkgo biloba extract (GBE) with preventive effect against diabetic nephropathy (DN) was developed using mesangial cells extraction coupled with high‐performance liquid chromatography tandem mass spectrometry (LC‐MS/MS) analysis. Mesangial cells were first divided into two groups according to their treatments with high glucose or high glucose plus GBE. After incubation for 4, 8, 12, 16, 24 and 48 h, the cells were harvested and extracted with 40% acetic acid in water before LC‐MS/MS analysis. Then, 19 compounds and five metabolites were found to selectively combine with mesangial cells. Notably, compounds including quercetin and rutin were identified or tentatively characterized according to the results of retention time and MS spectra, which is highly consistent with our previous reports that quercetin and rutin are potent protective agents against glomerulosclerosis in DN. Therefore, all these results indicate that target cell extraction coupled with LC‐MS/MS analysis can be successfully applied for predicting the bioactive components in GBE with preventive effect against DN. Copyright © 2014 John Wiley & Sons, Ltd.     

A novel interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. The performance of the variable flow nanoscale LC/MS/MS interface is demonstrated by the automated analysis of standard peptide mixtures and protein digests utilizing variable flow, data-dependent scanning MS/MS techniques, and automated database searching.     

Analysis of Monoclonal Antibodies in Human Serum as a Model for Clinical Monoclonal Gammopathy by Use of 21 Tesla FT-ICR Top-Down and Middle-Down MS/MS

With the rapid growth of therapeutic monoclonal antibodies (mAbs), stringent quality control is needed to ensure clinical safety and efficacy. Monoclonal antibody primary sequence and post-translational modifications (PTM) are conventionally analyzed with labor-intensive, bottom-up tandem mass spectrometry (MS/MS), which is limited by incomplete peptide sequence coverage and introduction of artifacts during the lengthy analysis procedure. Here, we describe top-down and middle-down approaches with the advantages of fast sample preparation with minimal artifacts, ultrahigh mass accuracy, and extensive residue cleavages by use of 21 tesla FT-ICR MS/MS. The ultrahigh mass accuracy yields an RMS error of 0.2–0.4 ppm for antibody light chain, heavy chain, heavy chain Fc/2, and Fd subunits. The corresponding sequence coverages are 81%, 38%, 72%, and 65% with MS/MS RMS error ~4 ppm. Extension to a monoclonal antibody in human serum as a monoclonal gammopathy model yielded 53% sequence coverage from two nano-LC MS/MS runs. A blind analysis of five therapeutic monoclonal antibodies at clinically relevant concentrations in human serum resulted in correct identification of all five antibodies. Nano-LC 21 T FT-ICR MS/MS provides nonpareil mass resolution, mass accuracy, and sequence coverage for mAbs, and sets a benchmark for MS/MS analysis of multiple mAbs in serum. This is the first time that extensive cleavages for both variable and constant regions have been achieved for mAbs in a human serum background.

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石油芳烃组分中未知化合物——三叔丁基苯基磷酸酯的高分辨质谱分析

将大气压光电离(APPI)、电喷雾(ESI)、实时直接分析(DART)多种电离源和傅立叶变换离子回旋共振质谱(FT-ICR MS)联用对石油芳烃样品中的未知化合物进行研究。通过高分辨质谱的精确质量,结合碰撞诱导解离(CAD)技术,经分析并与文献标准物质谱图比对,推断未知物为三(2,4-二-叔丁基苯基)磷酸酯(TDTBPP),并研究了其在不同大气压电离源中的电离特性。APPI谱图中主要为[M+H]~+峰,同时存在M.~+峰。ESI谱图中主要为[M+Na]~+(不加甲酸)或[M+NH4]~+峰(加甲酸)。DART谱图中主要为[M+NH4]~+峰,而EI谱图中基峰为m/z 57(叔丁基),次强峰为[M-CH3]~+峰。     

An improved model potential for liquid lithium

An improvement in the computed structure of liquid lithium was obtained by adding the Xα Slater exchange energy to the electron pseudopotential of Ashcroft, Singwi, Sjölander et al. The remaining discrepancies can only be corrected by using a fully non-local pseudopotential for lithium, and perhaps by improving experimental accuracies of structure factors.     

Changes in zeta potential caused by a dc electric current for thin double layers

An asymptotic solution was obtained to describe one-dimensional, steady-state transport of a symmetric binary electrolyte normal to two large parallel electrodes, in the limit in which the Debye length is infinitesimal compared to the distance separating the two electrodes. Despite the nonzero ion flux, Boltzmann's equation continues to describe the relationship between either ion concentration and the electrostatic potential inside the diffuse part of the double layer, while local electroneutrality applies outside, even for current densities approaching the limiting value. In the absence of ion adsorption or dissociation reactions at the electrodes, the magnitude of any charge or zeta potential arising on the electrodes at zero current is determined by the equilibrium constant for the redox reactions which would exchange ionic charge carriers for electric charge carriers at the electrode surface. Nonzero current causes the ionic strength of the bulk to vary with position. This perturbs the Debye length of the diffuse cloud on either electrode: it is the local ionic strength just outside the cloud which determines the Debye length for that cloud. Nonzero current also changes the zeta potential. The dimensionless rate of change dζ/dJ was as large as 30.     

Platination of superoxide dismutase with cisplatin: tracking the ammonia ligands using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)

The high mass accuracy of FT-ICR MS combined with (15)N-labelling shows that mono- and di- platinated products from the reaction of erythrocyte superoxide dismutase with the anticancer drug cisplatin in solution retain their ammine ligands, in contrast to a recent X-ray crystallographic study.     

A Li-air fuel cell with recycle aqueous electrolyte for improved stability

A lithium-air fuel cell with a new designed cell structure for improved stability is proposed. The cell consists of two subunits: an energy conversion unit that employs a cation exchange membrane and a reaction-product recycling unit that collects/removes LiOH and thus protects the LISICON plate from corrosion under strong alkaline conditions. The aqueous electrolyte recycling system allows the newly structured Li-air fuel cell to attain higher theoretical energy density, and hence potential application as an alternative energy source for transportation.     

An improved cell for in-situ electrochemical ESR

An improved cell for simultaneous electrochemical ESR based on a coaxial cylindrical cavity is described and shown to have high sensitivity whilst behaving as a satisfactory hydrodynamic electrode as evidenced by Tafel analysis, by Levich analysis and comparison with theory for the dependence of the ESR signal on electrode currents and electrolyte flow rate.     

An improved LC‐MS/MS method for quantitation of indapamide in whole blood: application for a bioequivalence study

An improved LC‐MS/MS method for the quantitation of indapamide in human whole blood was developed and validated. Indapamide‐d3 was used as internal standard (IS) and liquid–liquid extraction was employed for sample preparation. LC separation was performed on Synergi Polar RP‐column (50 × 4.6 mm i.d.; 4 µm) and mobile phase composed of methanol and 5 mm aqueous ammonium acetate containing 1 mm formic acid (60:40), at flow rate of 1 mL/min. The run time was 3.0 min and the injection volume was 20 μL. Mass spectrometric detection was performed using electrospray ion source in negative ionization mode, using the transitions m/z 364.0 → m/z 188.9 and m/z 367.0 → m/z 188.9 for indapamide and IS, respectively. Calibration curve was constructed over the range 0.25–50 ng/mL. The method was precise and accurate, and provided recovery rates >80% for indapamide and IS. The method was applied to determine blood concentrations of indapamide in a bioequivalence study with two sustained release tablet formulations. The 90% confidence interval for the geometric mean ratios for maximum concentration was 95.78% and for the area under the concentration–time curve it was 97.91%. The tested indapamide tablets (Eurofarma Laboratórios S.A.) were bioequivalent to Natrilix®, according to the rate and extent of absorption. Copyright © 2014 John Wiley & Sons, Ltd.     

Dissolved oxygen measurement with an improved amperometric cell

An improved amperometric cell for dissolved oxygen is described. The cathode material is directly deposited on the membrane in such a manner that the metal layer is sufficiently permeable for oxygen, but not porous. As there is no electrolyte layer between the cathode and the membrane, the signals are very stable. As the membrane is not subject to mechanical stresses, the diffusion pathlength, controlling the signal magnitude, is quite stable and so contributes to the overall stability of the response. This principle allows new constructions such as the flow-through cell.     

Triple mass spectrometry (MS/MS/MS) with a floated collision cell in a four-sector tandem mass spectrometer

A method is described for carrying out triple mass spectrometry (MS/MS/MS) experiments with an electrically floated collision cell in the third field-free region on a tandem double-focusing mass spectrometer. The method described may use magnet calibration obtained at any accelerating voltage and is generally applicable at any value of the collision cell voltage. The utility of the method to acquire MS/MS/MS spectra of enhanced quality is demonstrated on a JEOL JMS-HX110/HX110 four-sector mass spectrometer.     

Coupling porous sheathless interface MS with transient‐ITP in neutral capillaries for improved sensitivity in glycopeptide analysis

IgG antibodies are modulated in their function by the specific structure of the N‐glycans attached to their Fc (fragment crystallizable) portions. However, the glycosylation analysis of antigen‐specific IgGs is a challenging task as antibody levels to a given antigen only represent a fraction of the total IgG levels. Here, we investigated the use of a transient‐ITP (t‐ITP)—MS method for highly sensitive IgG1 glycosylation profiling as a complementary method to a high‐throughput nano‐RPLC‐MS method. It was found that t‐ITP‐CZE using neutrally coated separation capillaries with a large volume injection (37% of capillary volume) and interfaced to MS with a sheathless porous sprayer yielded a 40‐fold increase in sensitivity for IgG1 Fc glycopeptide analysis when compared to the conventional strategy. Furthermore, the glycoform profiles found with the t‐ITP‐CZE strategy were comparable to those from nano‐RPLC‐MS. In conclusion, the use of the highly sensitive t‐ITP‐CZE‐MS method will provide information on IgG Fc glycosylation for those samples with IgG1 concentrations below the LODs of the conventional method.