TL;DR: XCMS Online provides a solution for the complete untargeted metabolomic workflow including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization.
Abstract: Recently, interest in untargeted metabolomics has become prevalent in the general scientific community among an increasing number of investigators. The majority of these investigators, however, do not have the bioinformatic expertise that has been required to process metabolomic data by using command-line driven software programs. Here we introduce a novel platform to process untargeted metabolomic data that uses an intuitive graphical interface and does not require installation or technical expertise. This platform, called XCMS Online, is a web-based version of the widely used XCMS software that allows users to easily upload and process liquid chromatography/mass spectrometry data with only a few mouse clicks. XCMS Online provides a solution for the complete untargeted metabolomic workflow including feature detection, retention time correction, alignment, annotation, statistical analysis, and data visualization. Results can be browsed online in an interactive, customizable table showing statistics, chrom...
TL;DR: This chapter discusses the development of personalized medicine and home testing in the developing world, and some of the strategies used to achieve this goal have not yet been developed.
Abstract: Introduction A Why POC Diagnostics? B Time B Patient Responsibility and Compliance B Cost B Diagnostic Targets C Proteins C Metabolites and Other Small Molecules C Nucleic Acids C Human Cells D Microbes/Pathogens D Drugs and Food Safety D Current Context of POC Assays E POC Glucose Assays E Lateral Flow Assays E Limitations of “Traditional” POC Approaches F Enabling Technologies G Printing and Laminating G Microfluidic Technologies and Approaches: “Unit Operations” for POC Devices G Pumping and Valving H Mixing I Separation I Reagent Storage J Sample Preparation K Surface Chemistry and Device Substrates L Physical Adsorption L Bioaffinity Attachment L Covalent Attachment M Substrate Materials M Detection M Electrochemical Detection N Optical Detection N Magnetic Detection N Label-Free Methods O Enabling Multiplexed Assays O Recent Innovation O Lateral Flow Assay Technologies O Proteins P Antibodies P Protein Expression and Purification Q Nucleic Acids Q Aptamers R Infectious Diseases and Food/Water Safety R Blood Chemistry S Coagulation Markers S Whole Cells S Trends, Unmet Needs, Perspectives T Glucose T Global Health and the Developing World T Personalized Medicine and Home Testing U Technology Trends U Multiplexing V Author Information V Biographies V Acknowledgment W References W
TL;DR: CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data is presented, and a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate is presented.
Abstract: Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. W...
TL;DR: A simple, economical, and green preparative strategy toward water-soluble, fluorescent carbon nanoparticles (CPs) with a quantum yield of approximately 6.9% by hydrothermal process using low cost wastes of pomelo peel as a carbon source for the first time is reported.
Abstract: The present article reports on a simple, economical, and green preparative strategy toward water-soluble, fluorescent carbon nanoparticles (CPs) with a quantum yield of approximately 6.9% by hydrothermal process using low cost wastes of pomelo peel as a carbon source for the first time. We further explore the use of such CPs as probes for a fluorescent Hg2+ detection application, which is based on Hg2+-induced fluorescence quenching of CPs. This sensing system exhibits excellent sensitivity and selectivity toward Hg2+, and a detection limit as low as 0.23 nM is achieved. The practical use of this system for Hg2+ determination in lake water samples is also demonstrated successfully.
TL;DR: Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR).
Abstract: Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5% was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies.
TL;DR: It is demonstrated that this facile methodology can offer a rapid, reliable, and selective detection of Cu(2+) with a detection limit as low as 6 nM and a dynamic range from 10 to 1100 nM.
Abstract: A novel sensing system has been designed for Cu2+ ion detection based on the quenched fluorescence (FL) signal of branched poly(ethylenimine) (BPEI)-functionalized carbon quantum dots (CQDs) Cu2+ ions can be captured by the amino groups of the BPEI-CQDs to form an absorbent complex at the surface of CQDs, resulting in a strong quenching of the CQDs’ FL via an inner filter effect Herein, we have demonstrated that this facile methodology can offer a rapid, reliable, and selective detection of Cu2+ with a detection limit as low as 6 nM and a dynamic range from 10 to 1100 nM Furthermore, the detection results for Cu2+ ions in a river water sample obtained by this sensing system agreed well with that by inductively couple plasma mass spectrometry, suggesting the potential application of this sensing system
TL;DR: This study proposes a possible mechanism for sulfur reduction consisting of three steps, and investigates the electrolyte composition at different discharge potentials in a TEGDME-based electrolyte.
Abstract: The lithium/sulfur battery is a promising electrochemical system that has a high theoretical capacity of 1675 mAh g–1, but its discharge mechanism is well-known to be a complex multistep process. As the active material dissolves during cycling, this discharge mechanism was investigated through the electrolyte characterization. Using high-performance liquid chromatography, UV–visible absorption, and electron spin resonance spectroscopies, we investigated the electrolyte composition at different discharge potentials in a TEGDME-based electrolyte. In this study, we propose a possible mechanism for sulfur reduction consisting of three steps. Long polysulfide chains are produced during the first reduction step (2.4–2.2 V vs Li+/Li), such as S82– and S62–, as evidenced by UV and HPLC data. The S3•– radical can also be found in solution because of a disproportionation reaction. S42– is produced during the second reduction step (2.15–2.1 V vs Li+/Li), thus pointing out the gradual decrease of the polysulfide chai...
TL;DR: This review covers advances in electrochemical and biochemical sensor development and usage during 2010 and 2011 and focuses on novel methods and materials, with a particular focus on the increasing use of graphene sheets for sensor material development.
Abstract: This review covers advances in electrochemical and biochemical sensor development and usage during 2010 and 2011 In choosing scholarly articles to contribute to this review, special emphasis was placed on work published in the areas of reference electrodes, potentiometric sensors, voltammetric sensors, amperometric sensors, biosensors, immunosensors, and mass sensors In the past two years there have been a number of important papers, that do not fall into the general subsections contained within the larger sections Such novel advances are very important for the field of electrochemical sensors as they open up new avenues and methods for future research Each section above contains a subsection titled “Other Papers of Interest” that includes such articles and describes their importance to the field in general For example, while most electrochemical techniques for sensing analytes of interest are based on the changes in potential or current, Shan et al1 have developed a completely novel method for performing electrochemical measurements In their work, they report a method for imaging local electrochemical current using the optical signal of the electrode surface generated from a surface plasmon resonance (SPR) The electrochemical current image is based on the fact that the current density can be easily calculated from the local SPR signal The authors demonstrated this concept by imaging traces of TNT on a fingerprint on a gold substrate
Full articles and reviews were primarily amassed by searching the SciFinder Scholar and ISI Web of Knowledge Additional articles were found through alternate databases or by perusing analytical journals for pertinent publications Due to the reference limitation, only publications written in English were considered for inclusion Obviously, there have been more published accounts of groundbreaking work with electrochemical and biochemical sensors than those covered here This review is a small sampling of the available literature and not intended to cover every advance of the past two years The literature chosen focuses on new trends in materials, techniques, and clinically relevant applications of novel sensors To ensure proper coverage of these trends, theoretical publications and applications of previously reported sensor development were excluded
We want to remind our readers that this review is not intended to provide comprehensive coverage of electrochemical sensor development, but rather to provide a glimpse of the available depth of knowledge published in the past two years This review is meant to focus on novel methods and materials, with a particular focus on the increasing use of graphene sheets for sensor material development For readers seeking more information on the general principles behind electrochemical sensors and electrochemical methods, we recommend other sources with a broader scope2, 3 Electrochemical sensor research is continually providing new insights into a variety of fields and providing a breadth of relevant literature that is worthy of inclusion in this review Unfortunately, it is impossible to cover each publication and unintentional oversights are inevitable We sincerely apologize to the authors of electrochemical and biochemical sensor publications that were inadvertently overlooked
TL;DR: This work serves as a blueprint for expanding the multiplexing capacity of the TMT reagents to at least 10-plex and possibly up to 18-plex, and is able to quantify across eight samples simultaneously by combining the (13)C- and (15)N-containing reporter ions.
Abstract: Quantitative mass spectrometry methods offer near-comprehensive proteome coverage; however, these methods still suffer with regards to sample throughput. Multiplex quantitation via isobaric chemical tags (e.g., TMT and iTRAQ) provides an avenue for mass spectrometry-based proteome quantitation experiments to move away from simple binary comparisons and toward greater parallelization. Herein, we demonstrate a straightforward method for immediately expanding the throughput of the TMT isobaric reagents from 6-plex to 8-plex. This method is based upon our ability to resolve the isotopic shift that results from substituting a 15N for a 13C. In an accommodation to the preferred fragmentation pathways of ETD, the TMT-127 and -129 reagents were recently modified such that a 13C was exchanged for a 15N. As a result of this substitution, the new TMT reporter ions are 6.32 mDa lighter. Even though the mass difference between these reporter ion isotopologues is incredibly small, modern high-resolution and mass accura...
TL;DR: A method for automated peak assignment based on peak-shape analysis via singular value decomposition in combination with detailed least-squares modeling of local pre- and postinjection baselines is described, which results in improved detection limits for high-affinity or low-enthalpy binding reactions and significantly higher precision of the derived thermodynamic parameters.
Abstract: Isothermal titration calorimetry (ITC) is a powerful classical method that enables researchers in many fields to study the thermodynamics of molecular interactions. Primary ITC data comprise the temporal evolution of differential power reporting the heat of reaction during a series of injections of aliquots of a reactant into a sample cell. By integration of each injection peak, an isotherm can be constructed of total changes in enthalpy as a function of changes in solution composition, which is rich in thermodynamic information on the reaction. However, the signals from the injection peaks are superimposed by the stochastically varying time-course of the instrumental baseline power, limiting the precision of ITC isotherms. Here, we describe a method for automated peak assignment based on peak-shape analysis via singular value decomposition in combination with detailed least-squares modeling of local pre- and postinjection baselines. This approach can effectively filter out contributions of short-term noi...
TL;DR: It is discovered that ZnFe(2)O(4) magnetic nanoparticles (MNPs) possess intrinsic peroxidase-like activity and exhibit several advantages such as high catalytic efficiency, good stability, monodispersion, and rapid separation over other peroxIDase nanomimetics and horseradish per oxidase (HRP).
Abstract: In this paper, we discovered that ZnFe2O4 magnetic nanoparticles (MNPs) possess intrinsic peroxidase-like activity. ZnFe2O4 MNPs exhibit several advantages such as high catalytic efficiency, good stability, monodispersion, and rapid separation over other peroxidase nanomimetics and horseradish peroxidase (HRP). ZnFe2O4 MNPs were used as a colorimetric biosensor for the detection of urine glucose. This method is simple, inexpensive, highly sensitive, and selective for glucose detection using glucose oxidase (GOx) and ZnFe2O4 MNPs with a linear range from 1.25 × 10–6 to 1.875 × 10–5 mol L–1 with a detection limit of 3.0 × 10–7 mol L–1. The color change observable by the naked eyes based on the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) is the principle for the sensing of urine glucose level.
TL;DR: A paper-based analytical device (μPAD) has been developed for the detection of E. coli O157:H7, Salmonella Typhimurium, and L. monocytogenes in food samples as a screening system and is capable of detecting bacteria in concentrations in inoculated ready-to-eat (RTE) meat as low as 10 colony-forming units/cm(2).
Abstract: Foodborne pathogens are a major public health threat and financial burden for the food industry, individuals, and society, with an estimated 76 million cases of food-related illness occurring in the United States alone each year. Three of the most important causative bacterial agents of foodborne diseases are pathogenic strains of Escherichia coli, Salmonella spp., and Listeria monocytogenes, due to the severity and frequency of illness and disproportionally high number of fatalities. Their continued persistence in food has dictated the ongoing need for faster, simpler, and less expensive analytical systems capable of live pathogen detection in complex samples. Culture techniques for detection and identification of foodborne pathogens require 5–7 days to complete. Major improvements to molecular detection techniques have been introduced recently, including polymerase chain reaction (PCR). These methods can be tedious; require complex, expensive instrumentation; necessitate highly trained personnel; and ar...
TL;DR: This report presents a highly sensitive, rhodamine B-covered gold nanoparticle (RB-AuNP) -based assay with dual readouts (colorimetric and fluorometric) for detecting organophosphorus and carbamate pesticides in complex solutions.
Abstract: This report presents a highly sensitive, rhodamine B-covered gold nanoparticle (RB-AuNP) -based assay with dual readouts (colorimetric and fluorometric) for detecting organophosphorus and carbamate pesticides in complex solutions. The detection mechanism is based on the fact that these pesticides can inhibit the activity of acetylcholinesterase (AChE), thus preventing the generation of thiocholine (which turns the RB-AuNP solutions blue and unquenches the fluorescence of RB simultaneously). The color of the RB-AuNP solution remains red and the fluorescence of RB remains quenched. By use of this dual-readout assay, the lowest detectable concentrations for several kinds of pesticides including carbaryl, diazinon, malathion, and phorate were measured to be 0.1, 0.1, 0.3, and 1 μg/L, respectively, all of which are much lower than the maximum residue limits (MRL) as reported in the European Union pesticides database as well as those from the U.S. Department Agriculture (USDA). This assay allows detection of pe...
TL;DR: The shell thickness-dependent Raman enhancement of silver-coated gold nanoparticles (Au@Ag NPs) for the identification and detection of pesticide residues at various fruit peels is reported.
Abstract: Here, we report the shell thickness-dependent Raman enhancement of silver-coated gold nanoparticles (Au@Ag NPs) for the identification and detection of pesticide residues at various fruit peels. The Raman enhancement of Au@Ag NPs to a large family of sulfur-containing pesticides is ∼2 orders of magnitude stronger than those of bare Au and Ag NPs, and there is a strong dependence of the Raman enhancement on the Ag shell thickness. It has been shown for the first time that the huge Raman enhancement is contributed by individual Au@Ag NPs rather than aggregated Au@Ag NPs with “hot spots” among the neighboring NPs. Therefore, the Au@Ag NPs with excellent individual-particle enhancement can be exploited as stand-alone-particle Raman amplifiers for the surface identification and detection of pesticide residues at various peels of fruits, such as apple, grape, mango, pear, and peach. By casting the particle sensors onto fruit peels, several types of pesticide residues (e.g., thiocarbamate and organophosphorous c...
TL;DR: Under optimal conditions, the immuno-HCR assay presents good electrochemical responses for determination of target IgG at a concentration as low as 0.1 fg mL(-1), and can be further extended to the detection of other proteins or biomarkers.
Abstract: This work reports a novel electrochemical immunoassay protocol with signal amplification for determination of proteins (human IgG here used as a model target analyte) at an ultralow concentration using DNA-based hybridization chain reaction (HCR). The immuno-HCR assay consists of magnetic immunosensing probes, nanogold-labeled signal probes conjugated with the DNA initiator strands, and two different hairpin DNA molecules. The signal is amplified by the labeled ferrocene on the hairpin probes. In the presence of target IgG, the sandwiched immunocomplex can be formed between the immobilized antibodies on the magnetic beads and the signal antibodies on the gold nanoparticles. The carried DNA initiator strands open the hairpin DNA structures in sequence and propagate a chain reaction of hybridization events between two alternating hairpins to form a nicked double-helix. Numerous ferrocene molecules are formed on the neighboring probe, each of which produces an electrochemical signal within the applied potent...
TL;DR: The result agreed well with that by the DPD colorimetric method, suggesting the potential application of this new, green, sensitive, and facile sensing system in drinking water quality monitoring.
Abstract: Free chlorine was found to be able to destroy the passivated surface of the graphene quantum dots (GQDs) obtained by pyrolyzing citric acid, resulting in significant quenching of their fluorescence (FL) signal. After optimizing some experimental conditions (including response time, concentration of GQDs, and pH value of solution), a green and facile sensing system has been developed for the detection of free residual chlorine in water based on FL quenching of GQDs. The sensing system exhibits many advantages, such as short response time, excellent selectivity, wide linear response range, and high sensitivity. The linear response range of free chlorine (R2 = 0.992) was from 0.05 to 10 μM. The detection limit (S/N = 3) was as low as 0.05 μM, which is much lower than that of the most widely used N-N-diethyl-p-phenylenediamine (DPD) colorimetric method. This sensing system was finally used to detect free residual chlorine in local tap water samples. The result agreed well with that by the DPD colorimetric met...
TL;DR: The ability of T-wave IM spectrometry to differentiate diastereomers differing in Ω(N(2)) value by only 1 Å(2) is demonstrated, even though the resolution of these IM experiments were ∼40 (Ω/ΔΩ).
Abstract: We present the use of drug-like molecules as a traveling wave (T-wave) ion mobility (IM) calibration sample set, covering the m/z range of 122.1–609.3, the nitrogen collision cross-section (ΩN2) range of 124.5–254.3 A2 and the helium collision cross-section (ΩHe) range of 63.0–178.8 A2. Absolute ΩN2 and ΩHe values for the drug-like calibrants and two diastereomers were measured using a drift-tube instrument with radio frequency (RF) ion confinement. T-wave drift-times for the protonated diastereomers betamethasone and dexamethasone are reproducibly different. Calibration of these drift-times yields T-wave ΩN2 values of 189.4 and 190.4 A2, respectively. These results demonstrate the ability of T-wave IM spectrometry to differentiate diastereomers differing in ΩN2 value by only 1 A2, even though the resolution of these IM experiments were ∼40 (Ω/ΔΩ). Demonstrated through density functional theory optimized geometries and ionic electrostatic surface potential analysis, the small but measurable mobility diffe...
TL;DR: It is observed that the ECL intensity is efficiently quenched by trace amounts of Cu(2+), and it is anticipated that g-C(3)N(4) could be a new class of promising material for fabricating ECL sensors.
Abstract: This paper reports for the first time the electrogenerated chemiluminescence (ECL) behavior of graphite-like carbon nitride (g-C3N4) with K2S2O8 as the coreactant. The possible ECL reaction mechanisms are proposed. The spectral features of the ECL emission and photoluminescence (PL) of g-C3N4 are compared, and their resemblance demonstrates that the excited states of g-C3N4 from both ECL and photoexcitation are the same. The effects of K2S2O8 concentration, pH, g-C3N4/carbon powder ratio, and scan rate on the ECL intensity have been studied in detail. Furthermore, it is observed that the ECL intensity is efficiently quenched by trace amounts of Cu2+. g-C3N4 is thus employed to fabricate an ECL sensor which shows high selectivity to Cu2+ determination. The limit of detection is determined as 0.9 nM. It is anticipated that g-C3N4 could be a new class of promising material for fabricating ECL sensors.
TL;DR: Proof-in-principle is contributed that label-free microfluidic acoustophoresis can be used to enrich both viable and fixed cancer cells from WBCs with very high recovery and purity.
Abstract: Circulating tumor cells (CTC) are shed in peripheral blood at advanced metastatic stages of solid cancers. Surface-marker-based detection of CTC predicts recurrence and survival in colorectal, breast, and prostate cancer. However, scarcity and variation in size, morphology, expression profile, and antigen exposure impairs reliable detection and characterization of CTC. We have developed a noncontact, label-free microfluidic acoustophoresis method to separate prostate cancer cells from white blood cells (WBC) through forces generated by ultrasonic resonances in microfluidic channels. Implementation of cell prealignment in a temperature-stabilized (±0.5 °C) acoustophoresis microchannel dramatically enhanced the discriminatory capacity and enabled the separation of 5 μm microspheres from 7 μm microspheres with 99% purity. Next, we determined the feasibility of employing label-free microfluidic acoustophoresis to discriminate and divert tumor cells from WBCs using erythrocyte-lysed blood from healthy volunteers spiked with tumor cells from three prostate cancer cell-lines (DU145, PC3, LNCaP). For cells fixed with paraformaldehyde, cancer cell recovery ranged from 93.6% to 97.9% with purity ranging from 97.4% to 98.4%. There was no detectable loss of cell viability or cell proliferation subsequent to the exposure of viable tumor cells to acoustophoresis. For nonfixed, viable cells, tumor cell recovery ranged from 72.5% to 93.9% with purity ranging from 79.6% to 99.7%. These data contribute proof-in-principle that label-free microfluidic acoustophoresis can be used to enrich both viable and fixed cancer cells from WBCs with very high recovery and purity.
TL;DR: A paper-based microfluidic device that measures two enzymatic markers of liver function and total serum protein and shows standard deviations in calibration runs and "spiked" standards that are acceptable for routine clinical use is described.
Abstract: This paper describes a paper-based microfluidic device that measures two enzymatic markers of liver function (alkaline phosphatase, ALP, and aspartate aminotransferase, AST) and total serum protein. A device consists of four components: (i) a top plastic sheet, (ii) a filter membrane, (iii) a patterned paper chip containing the reagents necessary for analysis, and (iv) a bottom plastic sheet. The device performs both the sample preparation (separating blood plasma from erythrocytes) and the assays; it also enables both qualitative and quantitative analysis of data. The data obtained from the paper-microfluidic devices show standard deviations in calibration runs and “spiked” standards that are acceptable for routine clinical use. This device illustrates a type of test useable for a range of assays in resource-poor settings.
TL;DR: This work presents a comprehensive study aiming to evaluate current and novel matrix candidates for high spatial resolution MALDI imaging mass spectrometry of lipids from tissue section after deposition by sublimation, finding DAN to be of high efficiency providing rich lipid signatures in both positive and negative polarities with high vacuum stability and sub-20 μm resolution capacity.
Abstract: Matrix sublimation has demonstrated to be a powerful approach for high-resolution matrix-assisted laser desorption ionization (MALDI) imaging of lipids, providing very homogeneous solvent-free deposition. This work presents a comprehensive study aiming to evaluate current and novel matrix candidates for high spatial resolution MALDI imaging mass spectrometry of lipids from tissue section after deposition by sublimation. For this purpose, 12 matrices including 2,5-dihydroxybenzoic acid (DHB), sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA), 2,6-dihydroxyacetphenone (DHA), 2′,4′,6′-trihydroxyacetophenone (THAP), 3-hydroxypicolinic acid (3-HPA), 1,8-bis(dimethylamino)naphthalene (DMAN), 1,8,9-anthracentriol (DIT), 1,5-diaminonapthalene (DAN), p-nitroaniline (NIT), 9-aminoacridine (9-AA), and 2-mercaptobenzothiazole (MBT) were investigated for lipid detection efficiency in both positive and negative ionization modes, matrix interferences, and stability under vacuum. For the most relevant matrices, ...
TL;DR: It could be shown that a dilution of extracts by a factor of 25-40 reduces ion suppression to less than 20% if the initial suppression is ≤80%, and for stronger matrix effects or complete elimination of suppression, higher dilution factors were needed.
Abstract: In this study, the relationship between matrix concentration and suppression of electrospray ionization (matrix effects) was investigated. Ion suppression of pesticides present in QuEChERS extracts was used as an example. Residue-free extracts of four different commodities, avocado, black tea, orange, and rocket (arugula), were fortified with 39 pesticides each. For many of the resulting 156 pesticide/matrix combinations, considerable matrix effects were observed if the coextracted matrix of 8 mg of equivalent sample (in the case of tea: 1.6 mg) was injected with the undiluted extracts. The reduction of these matrix effects was measured at 10 levels of dilution up to 1000-fold. The results obtained indicate a linear correlation between matrix effects and the logarithm of matrix concentration (or dilution factor) until the zero-effect level of further dilution was reached. Using the logarithmic equations, it could be shown that a dilution of extracts by a factor of 25–40 reduces ion suppression to less tha...
TL;DR: The principle of the binding-induced DNA hybridization and fluorescence enhancement of Ag NCs can be extended to other homogeneous assay applications provided that two appropriate probes are available to bind with the same target molecule.
Abstract: We present here a binding-induced fluorescence turn-on assay for protein detection. Key features of this assay include affinity binding-induced DNA hybridization and fluorescence enhancement of silver nanoclusters (Ag NCs) using guanine-rich DNA sequences. In an example of an assay for human α-thrombin, two aptamers (Apt15 and Apt29) were used and were modified by including additional sequence elements. A 12-nucleotide (nt) sequence was used to link the first aptamer with a nanocluster nucleation sequence at the 5′-end. The second aptamer was linked through a complementary sequence (12-nt) to a G-rich overhang at the 3′-end. Binding of the two aptamer probes to the target protein initiates hybridization between the complementary linker sequences attached to each aptamer and thereby bring the end of the G-rich overhang to close proximity to Ag NCs, resulting in a significant fluorescence enhancement. With this approach, a detection limit of 1 nM and a linear dynamic range of 5 nM–2 μM were achieved for hum...
TL;DR: The basic principles, practices, and pitfalls in the process of compound identification by searching mass spectral reference libraries are presented and more general concerns and the problem of "unknown unknowns" are explored.
Abstract: The basic principles, practices, and pitfalls in the process of compound identification by searching mass spectral reference libraries are presented. Factors affecting the identification process are discussed as members of one of three major contributors to identification confidence: prior probability, risk of false negative results, and risk of false positive results. More general concerns and the problem of "unknown unknowns" are then explored.
TL;DR: A protocol enabling consecutive digestion of the sample with two or three enzymes, MED-FASP offers efficient exploration of previously unused sample material, increasing depth of proteomic analyses and sequence coverage.
Abstract: Analytical advantages of using multiple enzymes for sample digestion (MED), primarily an increase of sequence coverage, have been reported in several studies. However, this approach is only rarely used, mainly because it requires additional sample and mass spectrometric measurement time. We have previously described Filter Aided Sample Preparation (FASP), a type of proteomic reactor, in which samples dissolved in sodium dodecyl sulfate (SDS) are digested in an ultrafiltration unit. In FASP, such as in any other preparation protocol, a portion of sample remains after digestion and peptide elution. Making use of this fact, we here develop a protocol enabling consecutive digestion of the sample with two or three enzymes. By use of the FASP method, peptides are liberated after each digestion step and remaining material is subsequently cleaved with the next proteinase. We observed excellent performance of the ultrafiltration devices in this mode, allowing efficient separation of orthogonal populations of pepti...
TL;DR: On the basis of an aggregation-induced fluorescence quenching mechanism, these fluorescent AuNCs offer acceptable sensitivity, high selectivity, and a limit of detection of 3.5 μM for the determination of Fe(3+) ions, which is lower than the maximum level permitted in drinking water by the U.S. Environmental Protection Agency.
Abstract: In this paper, we describe a simple one-pot method, employing l-3,4-dihydroxyphenylalanine (l-DOPA) as a reducing/capping reagent, for the synthesis of fluorescent gold nanoclusters (AuNCs). Within a short reaction time of 15 min (excluding the time required for purification), this strategy allows the fabrication of homogeneous AuNCs having the capability to sense ferric ions (Fe3+). The as-prepared AuNCs exhibited a fluorescence emission at 525 nm and a quantum yield of 1.7%. On the basis of an aggregation-induced fluorescence quenching mechanism, these fluorescent AuNCs offer acceptable sensitivity, high selectivity, and a limit of detection of 3.5 μM for the determination of Fe3+ ions, which is lower than the maximum level (0.3 mg L–1, equivalent to 5.4 μM) of Fe3+ permitted in drinking water by the U.S. Environmental Protection Agency.
TL;DR: The multiplexed nanoflare is a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell, and one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background.
Abstract: We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are spherical nucleic acid (SNA) gold nanoparticle (Au NP) conjugates consisting of densely packed and highly oriented oligonucleotide sequences, many of which are hybridized to a reporter with a distinct fluorophore label and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra- and intracellular environments. Importantly, one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background. Compared to single-component nanoflares, these structures allow one to determine more precisely relative mRNA levels in individual cells, improving cell sorting and quantification.
TL;DR: The detection capabilities of single particle inductively coupled plasma-mass spectrometry with respect to particle size and number concentrations are investigated and the potential of spICPMS for environmental detection of nanoparticles is demonstrated for a wastewater treatment plant effluent sample.
Abstract: The detection capabilities of single particle inductively coupled plasma-mass spectrometry (spICPMS) with respect to particle size and number concentrations are investigated for the case of silver nanoparticles (ca. 20–80 nm). An iterative algorithm was developed where particle measurement events were distinguished as outliers from the more continuous dissolved ion signal if the measured intensity was more than five times the standard deviation of the whole data set. The optimal dwell time for 40–80 nm particles, limiting both incomplete and multiple particle events, was 5 ms. The smallest detectable particle size (ca. 20 nm) is mainly limited by the overlap of particle events and dissolved signal that increases with noise on both signals. The lowest measurable number concentration is limited by the relative frequency of erroneously identified particle events, a limit that can be reduced by acquiring more data points. Finally, the potential of spICPMS for environmental detection of nanoparticles is demons...
TL;DR: The development of a point-of-care immunosensor for the detection of the cancer biomarker (total prostate-specific antigen, tPSA) using surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) sensor platforms in human serum samples demonstrates the high potential of the developed sensor devices as platforms for clinical prostate cancer diagnosis and prognosis.
Abstract: Early detection of cancer is vital for the successful treatment of the disease. Hence, a rapid and sensitive diagnosis is essential before the cancer is spread out to the other body organs. Here we describe the development of a point-of-care immunosensor for the detection of the cancer biomarker (total prostate-specific antigen, tPSA) using surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) sensor platforms in human serum samples. KD of the antibody used toward PSA was calculated as 9.46 × 10–10 M, indicating high affinity of the antibody used in developing the assay. By performing a sandwich assay using antibody-modified nanoparticles concentrations of 2.3 ng mL–1 (Au, 20 nm) and 0.29 ng mL–1 (8.5 pM) (Au, 40 nm) tPSA in 75% human serum were detected using the developed assay on an SPR sensor chip. The SPR sensor results were found to be comparable to that achieved using a QCM sensor platform, indicating that both systems can be applied for disease biomarkers screening. The clinical ap...