Next-Generation Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Source for Mass Spectrometry Imaging and High-Throughput Screening.

Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a hybrid, ambient ionization source that combines the advantages of electrospray ionization and matrix-assisted laser desorption/ionization, making it a versatile tool for both high-throughput screening (HTS) and mass spectrometry imaging (MSI) studies. To expand the capabilities of the IR-MALDESI source, an entirely new architecture was designed to overcome the key limitations of the previous source. This next-generation (NextGen) IR-MALDESI source features a vertically mounted IR-laser, a planar translation stage with computerized sample height control, an aluminum enclosure, and a novel mass spectrometer interface plate. The NextGen IR-MALDESI source has improved user-friendliness, improved overall versatility, and can be coupled to numerous Orbitrap mass spectrometers to accommodate more research laboratories. In this work, we highlight the benefits of the NextGen IR-MALDESI source as an improved platform for MSI and direct analysis. We also optimize the NextGen MALDESI source component geometries to increase target ion abundances over a wide m/z range. Finally, documentation is provided for each NextGen IR-MALDESI part so that it can be replicated and incorporated into any lab space.

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.

Multiplexed, isobaric tagging methods are powerful techniques to increase throughput, precision, and accuracy in quantitative proteomics. The dynamic range and accuracy of quantitation, however, can be limited by coisolation of tag-containing peptides that release reporter ions and conflate quantitative measurements across precursors. Methods to alleviate these effects often lead to the loss of protein and peptide identifications through online or offline filtering of interference containing spectra. To alleviate this effect, high-Field Asymmetric-waveform Ion Mobility Spectroscopy (FAIMS) has been proposed as a method to reduce precursor coisolation and improve the accuracy and dynamic range of multiplex quantitation. Here we tested the use of FAIMS to improve quantitative accuracy using previously established TMT-based interference standards (triple-knockout [TKO] and Human-Yeast Proteomics Resource [HYPER]). We observed that FAIMS robustly improved the quantitative accuracy of both high-resolution MS2 (HRMS2) and synchronous precursor selection MS3 (SPS-MS3)-based methods without sacrificing protein identifications. We further optimized and characterized the main factors that enable robust use of FAIMS for multiplexed quantitation. We highlight these factors and provide method recommendations to take advantage of FAIMS technology to improve isobaric-tag-quantification moving forward.

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.

Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI-FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. A 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.

Numerical simulation of ion transport in an atmosphere-to-vacuum interface taking into account gas dynamics and space charge.

A two-step approach was developed for the study of ion transport in an atmospheric pressure interface. In the first step, the flow in the interface was numerically simulated using the standard gas dynamic package ANSYS CFX 15.0. In the second step, the calculated fields of pressure, temperature, and velocity were imported into a custom-built software application for simulation of ion motion under the influence of both gas dynamic and electrostatic forces. To account for space charge effects in axially symmetric interfaces an analytical expression was used for the Coulomb force. For all other types of interfaces, an iterative approach for the Coulomb force computation was developed. The simulations show that the influence of the space charge is the main contributor to the loss of ion current in the heated capillary. In addition, the maximum ion current which can be transmitted through the heated capillary (0.58 mm inner diameter and 58.5 mm length) is limited to ∼6 nA for ions with m/z = 508 Da and with reduced ion mobility 1.05 cm2V-1s-1. This limit remains practically constant and independent of the ion current at the entrance of the capillary. For a particular ion type, this limit depends on its m/z ratio and ion mobility.

Age-Related Deterioration of Perineuronal Nets in the Primary Auditory Cortex of Mice.

Age-related changes in inhibitory neurotransmission in sensory cortex may underlie deficits in sensory function. Perineuronal nets (PNNs) are extracellular matrix components that ensheath some inhibitory neurons, particularly parvalbumin positive (PV+) interneurons. PNNs may protect PV+ cells from oxidative stress and help establish their rapid spiking properties. Although PNN expression has been well characterized during development, possible changes in aging sensory cortex have not been investigated. Here we tested the hypothesis that PNN+, PV+ and PV/PNN co-localized cell densities decline with age in the primary auditory cortex (A1). This hypothesis was tested using immunohistochemistry in two strains of mice (C57BL/6 and CBA/CaJ) with different susceptibility to age-related hearing loss and at three different age ranges (1-3, 6-8 and 14-24 months old). We report that PNN+ and PV/PNN co-localized cell densities decline significantly with age in A1 in both mouse strains. In the PNN+ cells that remain in the old group, the intensity of PNN staining is reduced in the C57 strain, but not the CBA strain. PV+ cell density also declines only in the C57, but not the CBA, mouse suggesting a potential exacerbation of age-effects by hearing loss in the PV/PNN system. Taken together, these data suggest that PNN deterioration may be a key component of altered inhibition in the aging sensory cortex, that may lead to altered synaptic function, susceptibility to oxidative stress and processing deficits.

Advancement of atmospheric-vacuum interfaces for mass spectrometers with a focus on increasing gas throughput for improving sensitivity.

Ion sampling from an electrospray ionization (ESI) source was improved by increasing gas conductance of the MS inlet by 4.3-fold. Converting the gas throughput (Q) into sensitivity improvement was dependent on ion desolvation and handling of the gas load. Desolvation was addressed by using a novel slot shaped inlet that exhibited desolvation properties identical to the 0.58 mm i.d capillary. An assay tailored for "small molecules" at high chromatographic flow rate (500 µL/min) yielded a compound dependent 6.5 to 14-fold signal gain while analysis at nano chromatographic flow rate (300 nL/min) showed 2 to 3.5-fold improvement for doubly charged peptides. Improvement exceeding the Q (4.3-fold) at high chromatographic flow rate was explained by superior sampling of the spatially dispersed ion spray when using the slot shaped capillary. Sensitivity improvement across a wide range of chromatographic flow rate confirmed no compromise in ion desolvation with the increase in Q. Another improvement included less overflow of gas into the mass analyzer from the foreline region owing to the slot shape of the capillary. By doubling the roughing pump capacity and operating the electrodynamic ion funnel (EDIF) at ∼4 Torr, a single pumping stage was sufficient to handle the gas load. The transport of solvent clusters from the LC effluent into the mass analyzer was prevented by a "wavy shaped" transfer quadrupole and was compared with a benchmark approach that delivered ions orthogonally into a differentially pumped dual EDIF at comparable gas Q.

Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.

The Antarctic continent is largely covered by an expansive ice sheet, but it harbors diverse terrestrial and aquatic habitats in the coastal ice-free continental margins. Here we present the draft genome of Microbacterium sp. CH12i, which was isolated from hypersaline, alkaline, and nutrient-rich groundwater from Cape Hallett, northern Victoria Land, Antarctica.

Functional expression of a penicillin acylase from the extreme thermophile Thermus thermophilus HB27 in Escherichia coli.

BACKGROUND: Penicillin acylases (PACs) are enzymes of industrial relevance in the manufacture of ß-lactam antibiotics. Development of a PAC with a longer half-life under the reaction conditions used is essential for the improvement of the operational stability of the process. A gene encoding a homologue to Escherichia coli PAC was found in the genome of the thermophilic bacterium Thermus thermophilus (Tth) HB27. Because of the nature of this PAC and its complex maturation that is crucial to reach its functional heterodimeric final conformation, the overexpression of this enzyme in a heterologous mesophilic host was a challenge. Here we describe the purification and characterization of the PAC protein from Tth HB27 overexpressed in Escherichia coli. RESULTS: Fusions to a superfolder green fluorescent protein and differential membrane solubilization assays indicated that the native enzyme remains attached through its amino-terminal end to the outer side of the cytoplasmic membrane of Tth cells. In order to overexpress this PAC in E. coli cells, a variant of the protein devoid of its membrane anchoring segment was constructed. The effect of the co-expression of chaperones and calcium supplementation of the culture medium was investigated. The total production of PAC was enhanced by the presence of DnaK/J and GrpE and even more by trigger factor and GroEL/ES. In addition, 10 mM calcium markedly improved both PAC specific and volumetric activities. Recombinant PAC was affinity-purified and proper maturation of the protein was confirmed by SDS-PAGE and MALDI-TOF analysis of the subunits. The recombinant protein was tested for activity towards several penicillins, cephalosporins and homoserine lactones. Hydrophobic acyl-chain penicillins were preferred over the rest of the substrates. Penicillin K (octanoyl penicillin) was the best substrate, with the highest specificity constant value (16.12 mM-1.seg-1). The optimum pH was aprox. 4 and the optimum temperature was 75 °C. The half-life of the enzyme at this temperature was 9.2 h. CONCLUSIONS: This is the first report concerning the heterologous expression of a pac gene from a thermophilic microorganism in the mesophilic host E. coli. The recombinant protein was identified as a penicillin K-deacylating thermozyme.

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

Since its introduction a few years ago, the linear ion trap Orbitrap (LTQ Orbitrap) instrument has become a powerful tool in proteomics research. For high resolution mass spectrometry measurements ions are accumulated in the linear ion trap and passed on to the Orbitrap analyzer. Simultaneously with acquisition of this signal, the major peaks are isolated in turn, fragmented and recorded at high sensitivity in the linear ion trap, combining the strengths of both mass analyzer technologies. Here we describe a next generation LTQ Orbitrap system termed Velos, with significantly increased sensitivity and scan speed. This is achieved by a vacuum interface using a stacked ring radio frequency ion guide with 10-fold higher transfer efficiency in MS/MS mode and 3-5-fold in full scan spectra, by a dual pressure ion trap configuration, and by reduction of overhead times between scans. The first ion trap efficiently captures and fragments ions at relatively high pressure whereas the second ion trap realizes extremely fast scan speeds at reduced pressure. Ion injection times for MS/MS are predicted from full scans instead of performing automatic gain control scans. Together these improvements routinely enable acquisition of up to ten fragmentation spectra per second. Furthermore, an improved higher-energy collisional dissociation cell with increased ion extraction capabilities was implemented. Higher-collision energy dissociation with high mass accuracy Orbitrap readout is as sensitive as ion trap MS/MS scans in the previous generation of the instrument.

Orbital alignment in N2O photodissociation. I. Determination of all even rank anisotropy parameters.

We present a general method for determination of the photofragment K=4 state multipoles in an ion imaging experiment. These multipoles are important for determining the full density matrix for any photofragment with j(a)> or =2. They are expressed in terms of laboratory frame anisotropy parameters that have distinct physical origins and possess characteristic angular distributions. The explicit expression for the (2+1) resonant multiphoton ionization absorption signal for the case of arbitrarily polarized probe light is derived and a procedure for isolation of the rank-4 state multipoles from all others is shown. This treatment is applied to the case of O((1)D) produced in the 193 nm photodissociation of N2O. The results show nonzero values for all K=4 anisotropy parameters, indicating the complexity of the photodissociation dynamics in this system.

Influence of test protocol in determining the blood response to model polymers.

A multi-parametric, multi-center evaluation of three polymers was performed measuring their response to blood contact. The purpose of this study was to pinpoint differences in tests performed for assessing "basic" hemocompatibility on identical materials at different centers and attempt to rationalize. Assays for platelet adhesion, activation, aggregability and activation of the coagulation system in addition to an ex vivo patency assay were performed at four centers across Europe, using protocols favored by each center for determining the blood-contacting performance of a biomaterial. Three polymers were chosen for their expected blood response spanning the range of undesirable to desirable: ethylenevinylacetate (EVA), polyvinylchloride (PVC) and PVC modified with polyethylene oxide (PEO). The assays were ranked in terms of their efficacy compared to cost and simplicity. A correlation between assays was calculated, indicating the ability of one test to correctly determine the blood response compared to another. Some assays were unable to distinguish between materials, but of the assays which could, the materials were ranked in the following order: EVA; PVC; PVC-PEO, EVA producing the most undesirable response. It is concluded that many commonly used assays for determining hemocompatibility are inappropriate, but there are simple and reliable test methods available which correlate well with the more sophisticated protocols.

Current and future issues in sensitisation testing.

Sensitisation is one of the biological risks that needs to be addressed for any medical device before clearance or clinical evaluation. This article describes the state of the art for this evaluation and also new variants of the procedure to increase the accuracy of these tests, particularly when some metals, latex-based products and macromolecular proteins such as collagen are concerned.

Biomaterial-induced sarcoma: A novel model to study preneoplastic change.

In the study of carcinogenesis most interest has focused on carcinomas, as they represent the majority of human cancers. The recognition of the adenoma-carcinoma sequence both in humans and in animal experimental models has given the field of basic oncology the opportunity to elucidate individual mechanisms in the multistep development of carcinoma. The relative scarcity of human sarcomas coupled with the lack of adequate animal models has hampered understanding of the molecular genetic steps involved. We present an experimental model in the rat in which a high incidence of malignant mesenchymal tumors arise around a subcutaneously implanted biomaterial. Nine commercially available biomaterials were implanted in a total of 490 rats of the Fischer strain for 2 years. On average, macroscopic tumors were found in 25.8% of implantation sites over a period from 26 to 110 weeks after implantation. The most frequent tumors were malignant fibrous histiocytomas and pleomorphic sarcomas, although fibrosarcomas, leiomyosarcomas, and angiosarcomas readily developed, the latter especially around polyurethane implants. Of particular interest are the results of a detailed histological study of the capsules around the implanted biomaterials without tumors. Here a spectrum of change from focal proliferative lesions through preneoplastic proliferation to incipient sarcoma could be observed. A parallel immunohistochemical study of peri-implant capsules showed that proliferating cell nuclear antigen was of particular help in identifying these atypical proliferative lesions. To our knowledge this is the first description of a sarcoma model in which preneoplastic lesions can be readily identified and also reproducibly induced. This model provides the molecular biologist with defined stages in the development of mesenchymal malignancy, with which the multistage tumorigenesis hypothesis can be tested, analogous to the well-known adenoma-carcinoma sequence.

From cytotoxicity to biocompatibility testing in vitro: cell adhesion molecule expression defines a new set of parameters.

Determination of potential cytotoxicity is a central issue in current biocompatibility testing standards such as ISO and ASTM. Most of these tests do not assess biocompatibility of a biomaterial with regard to cell function. This study was aimed at screening a number of potential parameters that could be included in assessment of cell functional aspects of biocompatibility. Human umbilical vein endothelial cells (HUVEC) were seeded directly on titanium, NiCr alloy, CoCr alloy, PMMA, PE, PU, PVC, and silicone, or were exposed to the material extracts. Cytotoxicity was assessed for these materials through MTT conversion, crystal violet protein determination and Ki67 expression. In addition, expression of the cell adhesion molecules E-selectin, cadherin-5 and PECAM, as well as of the adhesion-associated proteins fibronectin and vinculin (focal adhesions), was determined by immunocytochemistry and western blotting. Cytotoxicity was not detected with the material extracts. Cells were able to adhere to bare metals, but not polymers. Fibronectin preadsorption resulted in adhesion and spreading also on the polymers. Cells were able to establish cell-cell contacts and focal adhesions. Western blotting, in combination with differential detergent extraction, indicated that linkage of cell-cell adhesion markers to the cytoskeleton may be used as an additional parameter relevant to cell function.

In vitro biocompatibility evaluation of a heparinizable material (PUPA), based on polyurethane and poly(amido-amine) components.

The biocompatibility of a new heparinizable material based on polyurethane and poly(amido-amine) (PUPA) was evaluated both in the heparinized and non-heparinized forms. The quantity of heparin present on the material was measured using radiolabelled heparin and biological tests. Heparin release in plasma from heparinized PUPA was investigated using in vitro methods. The behaviour of PUPA towards cellular and plasmatic blood components was studied. The influence of sterilization on the cytocompatibility response of both heparinized and non-heparinized PUPA was investigated; gamma-rays were found to be a suitable method of sterilization as no toxic response was noticed.

Treatment of experimental carotid aneurysms by endoprosthesis implantation: preliminary report.

Four experimental aneurysms were treated by implantation of an endoprosthetic stent. The aneurysms were surgically created by grafting a venous pouch on the carotid artery of mongrel dogs. Aneurysm patency was assessed angiographically. Under systemic heparinization and via a transfemoral approach, the stent measuring 20 mm in length and 5 mm in diameter, was implanted in the lumen of the parent artery at the level of the aneurysmal neck. Good angiographic results were obtained immediately following implantation, showing exclusion of the aneurysm from the circulation. Patency of the parent vessel was preserved in all the experimental aneurysms treated. In one case an angiogram performed 30 days later showed the same findings with excellent tolerance of the device. The technique of endovascular treatment of experimental aneurysms by stent implantation appears feasible and safe in vivo. Further investigations are still necessary before clinical applications.

In vitro evaluation of inflammatory cell response after CF4 plasma surface modification of poly(methyl methacrylate) intraocular lenses.

The inflammatory cell response of tetrafluorocarbon (CF4) plasma surface modification of poly(methyl methacrylate) intraocular lenses (IOLs) was investigated in vitro. After two hours of lens contact with human granulocytes, scanning electron microscopy showed significantly less cell activation and granulocyte adhesion on the surface-modified IOL than on the untreated IOL (P < .01). The x-ray photo-electron spectroscopy analysis of the CF4 plasma surface modification demonstrated that new compounds containing fluorine were homogeneously grafted onto the PMMA lens surface, resulting in a marked increase of contact angle. These in vitro results must be confirmed by in vivo studies of CF4 plasma surface modification of IOLs.

Wound healing of burns in rats treated with a new amino acid copolymer membrane.

A new amino acid copolymer (leucine + methylglutamate) membrane which is moderately permeable to water vapour, impermeable to bacteria, non-biodegradable and stable, has been developed as a burn wound covering. In an experimental model in the rat, excised burn lesions were covered either with the membrane or with conventional petrolatum-impregnated gauze. Morphometric analyses and histological investigations performed on days 7, 14, 21 and 42, suggested a significantly increased rate of healing for wounds covered with the polymeric membrane as compared with those covered with impregnated gauze. No wound dessication, fluid retention or exudate was observed under the membrane due to its moderate permeability to water vapour. The wounds covered with impregnated gauze also showed a marked inflammatory response in the granulation tissue, which remained even at day 42. This appearance was very different from a normal dermis or a polymeric membrane treated dermis.