Showing papers by "Agilent Technologies published in 2017"
TL;DR: The Blueprint PD‐L1 IHC Assay Comparison Project revealed that three of the four assays were closely aligned on tumor cell staining whereas the fourth showed consistently fewer tumor cells stained, indicating that interchanging assays and cutoffs would lead to “misclassification” of PD‐ L1 status for some patients.
1,034 citations
TL;DR: Improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date.
Abstract: Collision cross section (CCS) measurements resulting from ion mobility–mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (DTCCSN2) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these DTCCSN2 values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method...
315 citations
University of Sydney1, University of California, Los Angeles2, Princess Margaret Cancer Centre3, Memorial Sloan Kettering Cancer Center4, Harvard University5, Yale University6, Samsung Medical Center7, Vanderbilt University8, Hebron University9, Merck & Co.10, Agilent Technologies11, Columbia University12
TL;DR: Pembrolizumab provides promising long-term OS benefit with a manageable safety profile for PD-L1-expressing treatment-naive advanced NSCLC, with greatest efficacy observed in patients with TPS ≥50%.
178 citations
TL;DR: This study applied a nontargeted metabolomics approach based on ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS) to comprehensively profile the characteristic metabolites of white tea.
136 citations
TL;DR: This study investigated the applicability of different techniques for fluorescence excitation/emission matrices data interpretations, including peak-picking method, fluorescence regional integration and PARAFAC modelling, to act as surrogates in predicting emerging trace organic compounds removal during conventional wastewater treatments.
118 citations
TL;DR: This work shows that ASM eliminates the major drawbacks of FSM including complex elution solvent profiles, baseline disturbances, and slow 2D re-equilibration and demonstrates improvements in 2D separation quality using both simple small molecule probes and degradants of heat-treated bovine insulin as case studies.
Abstract: Two-dimensional liquid chromatography (2D-LC) is increasingly being viewed as a viable tool for solving difficult separation problems, ranging from targeted separations of structurally similar molecules to untargeted separations of highly complex mixtures. In spite of this performance potential, though, many users find method development challenging and most frequently cite the “incompatibility” between the solvent systems used in the first and second dimensions as a major obstacle. This solvent strength related incompatibility can lead to severe peak distortion and loss of resolution and sensitivity in the second dimension. In this paper, we describe a novel approach to address the incompatibility problem, which we refer to as Active Solvent Modulation (ASM). This valve-based approach enables dilution of 1D effluent with weak solvent prior to transfer to the 2D column but without the need for additional instrument hardware. ASM is related to the concept we refer to as Fixed Solvent Modulation (FSM), with...
112 citations
TL;DR: This data acquisition strategy enables a simultaneous mixture of database-dependent targeted and nontargeted metabolomics in combination with improved accuracy in metabolite identification, increasing the quality of the biological information acquired in a metabolomics experiment.
Abstract: High-resolution mass spectrometry (HRMS)-based metabolomics approaches have made significant advances. However, metabolite identification is still a major challenge with significant bottleneck in translating metabolomics data into biological context. In the current study, a liquid chromatography (LC)–HRMS metabolomics method was developed using an all ion fragmentation (AIF) acquisition approach. To increase the specificity in metabolite annotation, four criteria were considered: (i) accurate mass (AM), (ii) retention time (RT), (iii) MS/MS spectrum, and (iv) product/precursor ion intensity ratios. We constructed an in-house mass spectral library of 408 metabolites containing AMRT and MS/MS spectra information at four collision energies. The percent relative standard deviations between ion ratios of a metabolite in an analytical standard vs sample matrix were used as an additional metric for establishing metabolite identity. A data processing method for targeted metabolite screening was then created, merg...
100 citations
TL;DR: This investigation into the use of ultrafast chiral chromatography as a second dimension for 2D chromatographic separations of chiral and achiral drugs and metabolites, constitutional isomers, stereoisomers, and organohalogenated species is reported.
Abstract: Chromatographic separation and analysis of complex mixtures of closely related species is one of the most challenging tasks in modern pharmaceutical analysis. In recent years, two-dimensional liquid chromatography (2D-LC) has become a valuable tool for improving peak capacity and selectivity. However, the relatively slow speed of chiral separations has limited the use of chiral stationary phases (CSPs) as the second dimension in 2D-LC, especially in the comprehensive mode. Realizing that the recent revolution in the field of ultrafast enantioselective chromatography could now provide significantly faster separations, we herein report an investigation into the use of ultrafast chiral chromatography as a second dimension for 2D chromatographic separations. In this study, excellent selectivity, peak shape, and repeatability were achieved by combining achiral and chiral narrow-bore columns (2.1 mm × 100 mm and 2.1 mm × 150 mm, sub-2 and 3 μm) in the first dimension with 4.6 mm × 30 mm and 4.6 mm × 50 mm colum...
96 citations
TL;DR: In this paper, an analytical method for the simultaneous determination of aflatoxins B 1, B 2, G 1, G 2, ochratoxin A, fumonisins B 2 and B 2, zearalenone, deoxynivalenol, T 2 toxin, and HT-2 toxin using rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed.
90 citations
TL;DR: A microfluidic method is developed to identify and quantify low-abundance IgG N-glycans and show some of these IgGs can be used as biomarkers for rheumatoid arthritis.
Abstract: N-linked glycans on immunoglobulin G (IgG) have been associated with pathogenesis of diseases and the therapeutic functions of antibody-based drugs; however, low-abundance species are difficult to detect. Here we show a glycomic approach to detect these species on human IgGs using a specialized microfluidic chip. We discover 20 sulfated and 4 acetylated N-glycans on IgGs. Using multiple reaction monitoring method, we precisely quantify these previously undetected low-abundance, trace and even ultra-trace N-glycans. From 277 patients with rheumatoid arthritis (RA) and 141 healthy individuals, we also identify N-glycan biomarkers for the classification of both rheumatoid factor (RF)-positive and negative RA patients, as well as anti-citrullinated protein antibodies (ACPA)-positive and negative RA patients. This approach may identify N-glycosylation-associated biomarkers for other autoimmune and infectious diseases and lead to the exploration of promising glycoforms for antibody therapeutics. Post-translational modifications can affect antibody function in health and disease, but identification of all variants is difficult using existing technologies. Here the authors develop a microfluidic method to identify and quantify low-abundance IgG N-glycans and show some of these IgGs can be used as biomarkers for rheumatoid arthritis.
85 citations
TL;DR: The results highlight the importance of analyzing water samples using multiple separation techniques and in multiple ionization modes to obtain a comprehensive chemical contaminant profile.
Abstract: Efficient strategies are required to implement comprehensive suspect screening methods using high-resolution mass spectrometry within environmental monitoring campaigns. In this study, both liquid and gas chromatography time-of-flight mass spectrometry (LC-QTOF-MS and GC-QTOF-MS) were used to screen for >5000 target and suspect compounds in the Sacramento–San Joaquin River Delta in Northern California. LC-QTOF-MS data were acquired in All-Ions fragmentation mode in both positive and negative electrospray ionization (ESI). LC suspects were identified using two accurate mass LC-QTOF-MS/MS libraries containing pesticides, pharmaceuticals, and other environmental contaminants and a custom exact mass database with predicted transformation products (TPs). The additional fragment information from the All-Ions acquisition improved the confirmation of the compound identity, with a low false positive rate (9%). Overall, 25 targets, 73 suspects, and 5 TPs were detected. GC-QTOF-MS extracts were run in negative chemi...
TL;DR: In this article, the authors highlight the need for quantitative flux analysis to study NO in tumors and review mechanisms that link NO to cancer hallmarks, with a perspective of co-targeting NO metabolism with first-line therapies for improved outcome.
Abstract: Nitric oxide (NO) is a signaling molecule with pleiotropic physiological roles in normal cells and pathophysiological roles in cancer. NO synthetase expression and NO synthesis are linked to altered metabolism, neoplasticity, invasiveness, chemoresistance, immune evasion, and ultimately to poor prognosis of cancer patients. Exogenous NO in the microenvironment facilitates paracrine signaling, mediates immune responses, and triggers angiogenesis. NO regulates posttranslational protein modifications, S-nitrosation, and genome-wide epigenetic modifications that can have both tumor-promoting and tumor-suppressing effects. We review mechanisms that link NO to cancer hallmarks, with a perspective of co-targeting NO metabolism with first-line therapies for improved outcome. We highlight the need for quantitative flux analysis to study NO in tumors.
TL;DR: In this article, the use of nanofiltration membrane with pre-ozonation for surface water brine treatment was shown to significantly reduce organic fouling potential, and the dominant fouling mechanism was cake filtration.
TL;DR: This data indicates that modulation of PD-L1 through “cell reprograming” or “ ‘spiking’ the immune response to anti-PD-1 therapy may occur through a number of mechanisms, including “self-consistency” and “ LTD”.
Abstract: e14589Background: Developing clinically relevant and highly reproducible scoring methods for PD-L1 to identify patients who will respond effectively to anti-PD-1 therapy is key in the development o...
TL;DR: Key roles are identified for the active site amino acid trio in determining OleTJE catalytic efficiency in alkene production and in regulating protein stability, heme iron coordination, and spin state.
TL;DR: In this paper, metabolic profiles of microtissues derived from normal organs (heart, kidney) were relatively consistent when compared to microtissue derived from the same organ, which correlated to histology.
Abstract: Metabolism is a compartmentalized process, and it is apparent in studying cancer that tumors, like normal tissues, demonstrate metabolic cooperation between different cell types. Metabolic profiling of cells in 2D culture systems often fails to reflect the metabolism occurring within tissues in vivo due to lack of other cell types and 3D interaction. We designed a tooling and methodology to metabolically profile and compare 2D cultures with cancer cell spheroids, and microtissue slices from tumors, and normal organs. We observed differences in the basal metabolism of 2D and 3D cell cultures in response to metabolic inhibitors, and chemotherapeutics. The metabolic profiles of microtissues derived from normal organs (heart, kidney) were relatively consistent when comparing microtissues derived from the same organ. Treatment of heart and kidney microtissues with cardio- or nephro-toxins had early and marked effects on tissue metabolism. In contrast, microtissues derived from different regions of the same tumors exhibited significant metabolic heterogeneity, which correlated to histology. Hence, metabolic profiling of complex microtissues is necessary to understand the effects of metabolic co-operation and how this interaction, not only can be targeted for treatment, but this method can be used as a reproducible, early and sensitive measure of drug toxicity.
TL;DR: This study is intended to help provide a guideline for the implementation of indicator/surrogate models for real-time monitoring of TOrC abatement with ozone processes and integrate them into a regulatory framework in water reuse.
TL;DR: The MEC method has been applied to three different atomic spectrometric techniques and the results were comparable with, and in several cases more accurate than, values obtained using the traditional external calibration, internal standardization, and standard additions methods.
TL;DR: A novel analytical method based on high-performance liquid chromatography (HPLC) coupled with inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) has been developed and successfully applied for the analysis of TBBPA/S and their derivatives in water samples with satisfactory recoveries.
TL;DR: Comparison of cleanup methods in the analysis of veterinary drug residues in bovine tissues showed that the EMR-L method provided cleaner extracts overall and improved results for several anthelmintics and tranquilizers compared to the d-SPE method, but the E MRL method gave lower recoveries for certain β-lactam antibiotics.
Abstract: Veterinary drug residues in animal-derived foods must be monitored to ensure food safety, verify proper veterinary practices, enforce legal limits in domestic and imported foods, and for other purposes. A common goal in drug residue analysis in foods is to achieve acceptable monitoring results for as many analytes as possible, with higher priority given to the drugs of most concern, in an efficient and robust manner. The U.S. Department of Agriculture has implemented a multiclass, multi-residue method based on sample preparation using dispersive solid phase extraction (d-SPE) for cleanup and ultrahigh-performance liquid chromatography-tandem quadrupole mass spectrometry (UHPLC-QQQ) for analysis of >120 drugs at regulatory levels of concern in animal tissues. Recently, a new cleanup product called "enhanced matrix removal for lipids" (EMR-L) was commercially introduced that used a unique chemical mechanism to remove lipids from extracts. Furthermore, high-resolution quadrupole-time-of-flight (Q/TOF) for (U)HPLC detection often yields higher selectivity than targeted QQQ analyzers while allowing retroactive processing of samples for other contaminants. In this study, the use of both d-SPE and EMR-L sample preparation and UHPLC-QQQ and UHPLC-Q/TOF analysis methods for shared spiked samples of bovine muscle, kidney, and liver was compared. The results showed that the EMR-L method provided cleaner extracts overall and improved results for several anthelmintics and tranquilizers compared to the d-SPE method, but the EMR-L method gave lower recoveries for certain β-lactam antibiotics. QQQ vs. Q/TOF detection showed similar mixed performance advantages depending on analytes and matrix interferences, with an advantage to Q/TOF for greater possible analytical scope and non-targeted data collection. Either combination of approaches may be used to meet monitoring purposes, with an edge in efficiency to d-SPE, but greater instrument robustness and less matrix effects when analyzing EMR-L extracts. Graphical abstract Comparison of cleanup methods in the analysis of veterinary drug residues in bovine tissues.
TL;DR: Results show that qIHC provides a sensitive, quantitative, accurate, and robust assay for measurement of protein expression in formalin-fixed, paraffin-embedded cell lines, and tissue.
TL;DR: This work reports enzyme fusion systems in which Streptomyces coelicolor alditol oxidase (AldO) is linked to OleTJE, and uses these fusion systems to generate novel products from secondary turnover of 2‐OH and 3‐OH myristic acid primary products, expanding the catalytic repertoire of OleTjE.
TL;DR: This method was proved to be simple, sensitive, and effective, which can be applied for large-scale pesticide screening and quantification in vegetable oils.
Abstract: In this study, a simple and high-throughput method for determination of 255 pesticides in vegetable oils was developed based on QuEChERS sample preparation method combined with gas chromatography–triple quadrupole mass spectrometry. Different clean-up approaches were tested: A, 150 mg PSA + 150 mg C18; B, 250 mg PSA + 250 mg C18; C, 250 mg PSA + 250 mg C18 + 15 mg GCB; D, 250 mg PSA + 250 mg C18 + 50 mg GCB; and E, EMR-LipidTM. Best clean-up capacity was observed for EMR clean-up. The extraction procedures and parameters, including extraction time, solvent/sample ratio, and buffer system, were also thoroughly investigated and optimized. The limits of quantification (LOQ) ranged between 5 and 50 μg kg−1, and for the majority of the pesticides the LOQs were 5 μg kg−1, which were below the regulatory MRLs. Most recoveries at seven spiking levels were in the range of 70–120 % with RSDs <20 % indicating satisfactory accuracy. The coefficient of determination (r
2) was >0.99 within the calibration linearity range of 2–500 μg L−1 for the majority of the pesticides. This method was proved to be simple, sensitive, and effective, which can be applied for large-scale pesticide screening and quantification in vegetable oils.
TL;DR: Investigation of the occurrence and levels of OTA in infant formula and infant cereal products available in the U.S. market found the highest incidence and concentrations were found in oat-based infant cereals, followed by mixed grain cereals.
TL;DR: Nicotine was found to be degraded by triplet-state organic matter (3OM*), thus indicating that electron transfer is a preferred reaction mechanism for photodegradation in wastewater effluent.
Abstract: Nicotine is a highly toxic tobacco alkaloid that is ubiquitous in wastewater effluent. For the first time, we report the identification of the products and the pathways for the photodegradation of nicotine in an effluent matrix under simulated solar irradiation. Nicotine was found to be degraded by triplet-state organic matter (3OM*), thus indicating that electron transfer is a preferred reaction mechanism. Using the multivariate statistical strategies orthogonal projection to latent structures discriminant analysis (OPLS-DA) and hierarchical clustering, 49 potential transformation products (TPs) of nicotine were successfully extracted from the water matrix via high-resolution ultrahigh-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UHPLC–QTOF-MS). Overall, 30 TPs, including 4 groups of nonseparated isomeric photo TPs, were identified with various levels of confidence based on the tandem mass spectrometry information on standard compounds and the isotope-labeling method (us...
TL;DR: A framework for automatic classification of regions of interest (ROI) containing either benign or cancerous colon tissue extracted from whole slide H&E stained images using cell nuclei features showed promising results.
Abstract: Currently, diagnosis of colon cancer is based on manual examination of histopathological images by a pathologist. This can be time consuming and interpretation of the images is subject to inter- and intra-observer variability. This may be improved by introducing a computer-aided diagnosis (CAD) system for automatic detection of cancer tissue within whole slide hematoxylin and eosin (H&E) stains. Cancer disrupts the normal control mechanisms of cell proliferation and differentiation, affecting the structure and appearance of the cells. Therefore, extracting features from segmented cell nuclei structures may provide useful information to detect cancer tissue. A framework for automatic classification of regions of interest (ROI) containing either benign or cancerous colon tissue extracted from whole slide H&E stained images using cell nuclei features was proposed. A total of 1,596 ROI's were extracted from 87 whole slide H&E stains (44 benign and 43 cancer). A cell nuclei segmentation algorithm consisting of color deconvolution, k-means clustering, local adaptive thresholding, and cell separation was performed within the ROI's to extract cell nuclei features. From the segmented cell nuclei structures a total of 750 texture and intensity-based features were extracted for classification of the ROI's. The nine most discriminative cell nuclei features were used in a random forest classifier to determine if the ROI's contained benign or cancer tissue. The ROI classification obtained an area under the curve (AUC) of 0.96, sensitivity of 0.88, specificity of 0.92, and accuracy of 0.91 using an optimized threshold. The developed framework showed promising results in using cell nuclei features to classify ROIs into containing benign or cancer tissue in H&E stained tissue samples. © 2017 International Society for Advancement of Cytometry.
TL;DR: It is noteworthy that both the untreated effluent and the identified compounds have low toxicity with respect to V. fischeri, suggesting that the heterogeneous photocatalysis may be a good alternative for treatment of wastewaters containing FIP and its TPs, since under this condition the power consumption during the treatment can be significantly reduced.
TL;DR: The addition of ion mobility dimension has increased the separation of compounds in complex biological matrixes and has the potential to largely improve the throughput of metabolomics analysis.
Abstract: A commercial liquid chromatography/drift tube ion mobility-mass spectrometer (LC/IM-MS) was evaluated for its utility in global metabolomics analysis Performance was assessed using 12 targeted metabolite standards where the limit of detection (LOD), linear dynamic range, resolving power, and collision cross section (Ω) are reported for each standard Data were collected in three different instrument operation modes: flow injection analysis with IM-MS (FIA/IM-MS), LC/MS, and LC/IM-MS Metabolomics analyses of human plasma and HaCaT cells were used to compare the above three operation modes LC/MS provides linearity in response, data processing automation, improved limits of detection, and ease of use Advantages of LC/IM-MS and FIA/IM-MS include the ability to develop mobility–mass trend lines for structurally similar biomolecules, increased peak capacity, reduction of chemical/matrix noise, improvement in signal-to-noise, and separations of isobar/isomer compounds that are not resolved by LC We further
TL;DR: The experimental results confirm the feasibility of translating fingerprinting method conditions while preserving the informative power of 2D peak patterns for sample classification and discrimination and limit the loss of fingerprinting information.
TL;DR: This technique, applicable to any cut tissue section, is capable of demonstrating the highly variable distribution of metals within an organ or system, and can be used to identify changes in metal homeostasis and absolute levels within fine anatomical structures.
Abstract: Metals are found ubiquitously throughout an organism, with their biological role dictated by both their chemical reactivity and abundance within a specific anatomical region. Within the brain, metals have a highly compartmentalized distribution, depending on the primary function they play within the central nervous system. Imaging the spatial distribution of metals has provided unique insight into the biochemical architecture of the brain, allowing direct correlation between neuroanatomical regions and their known function with regard to metal-dependent processes. In addition, several age-related neurological disorders feature disrupted metal homeostasis, which is often confined to small regions of the brain that are otherwise difficult to analyze. Here, we describe a comprehensive method for quantitatively imaging metals in the mouse brain, using laser ablation - inductively coupled plasma - mass spectrometry (LA-ICP-MS) and specially designed image processing software. Focusing on iron, copper and zinc, which are three of the most abundant and disease-relevant metals within the brain, we describe the essential steps in sample preparation, analysis, quantitative measurements and image processing to produce maps of metal distribution within the low micrometer resolution range. This technique, applicable to any cut tissue section, is capable of demonstrating the highly variable distribution of metals within an organ or system, and can be used to identify changes in metal homeostasis and absolute levels within fine anatomical structures.