Recent advances in peptide-based (bottom-up) quantitative proteomics and bioinformatics have opened unprecedented opportunities for extensive investigation of cellular proteomes and their dynamics. Here we discuss two approaches currently used to investigate the global dynamics of phosphorylation based on the isolation of phosphorylated proteins or peptides. We evaluate the accuracy of these methodologies to grasp the global dynamics of phosphorylation, and we raise awareness on ambiguities inherent to these analyses. We conclude that further development of targeted approaches should prevent inaccurate conclusions about the nature of biological regulations and in particular kinase-substrate networks.

Presented herein is a combined experimental and computational study of the gold nanoparticle (AuNP) inner filter effect on surface enhanced Raman spectroscopic (SERS) measurements. Using a bianalyte strategy in which dithiopurine (DTP) and ethanol were employed as the model analytes, we demonstrated that AuNPs enhance DTP’s Raman signal but attenuate ethanol’s Raman intensity. Combined time-resolved UV–vis and Raman measurements showed that AuNP aggregation has significant and an exactly opposite impact on the AuNP inner filter effect and SERS enhancement. This research provides critical new insights regarding SERS signal variation and offers a simple methodology for reliable determination of the SERS enhancement factors.

The combination of high-resolution LC–MS-based untargeted metabolomics with stable isotope tracing provides a global overview of the cellular fate of precursor metabolites. This methodology enables detection of putative metabolites from biological samples and simultaneous quantification of the pattern and extent of isotope labeling. Labeling of Trypanosoma brucei cell cultures with 50% uniformly 13C-labeled glucose demonstrated incorporation of glucose-derived carbon into 187 of 588 putatively identified metabolites in diverse pathways including carbohydrate, nucleotide, lipid, and amino acid metabolism. Labeling patterns confirmed the metabolic pathways responsible for the biosynthesis of many detected metabolites, and labeling was detected in unexpected metabolites, including two higher sugar phosphates annotated as octulose phosphate and nonulose phosphate. This untargeted approach to stable isotope tracing facilitates the biochemical analysis of known pathways and yields rapid identification of previously unexplored areas of metabolism.

We have demonstrated two significant benefits of dynamic surface enhanced raman spectroscopy (DSERS) measurements: removal of instrumental and normal Raman interferences in surface enhanced raman spectroscopy (SERS) spectroscopy and site-selective spectroscopy of adsorbate populations on SERS-active particles. Our first example of shelled nanoparticles at very low concentrations confirmed the benefit of DSERS for removal of an overwhelmingly strong solvent spectral interference. The second benefit, site selection, was demonstrated with 4-mercaptopyridine on bare Au nanoparticles to observe a small population of molecules that were spectroscopically unique from the large population of molecules on the particles. The DSERS spectrum originated from excess variance between a small population of adsorbates on the ensemble of nanoparticles.

Incorporation of isotopic tag onto peptides via chemical labeling is a popular approach for quantitative proteomics. Chemical labeling via solution based methods usually lead to a tedious process and sample loss because several sample preparation steps including buffer exchange and desalting are performed. In this study, a solid phase based labeling approach by integration of glycopeptide enrichment and stable isotope labeling on hydrazide beads was developed for relative quantification of protein glycosylation, by which enrichment, washing, labeling, and release of the glycopeptides were all performed on the hydrazide beads sequentially. This approach was proved to be accurate in quantitative glycoproteome analysis and have good linearity range with 2 orders of magnitude for quantification of glycopeptides. Compared with dimethyl labeling conventionally performed in solution, the developed approach has better enrichment recovery (10–330% improvement) and high detection sensitivity in which 42% of annotated glycosites (vs 26%) still can be quantified using only 10 μg of four standard glycoprotein mixtures and 400 μg of bovine serum album interference as starting sample. The applicability of the approach for quantitative glycopeptide profiling was also explored by differential analysis of glycoproteome between human normal serum and liver cancer serum.

A novel approach to porous polymer monoliths hypercrosslinked to obtain large surface areas and modified with zwitterionic functionalities through the attachment of gold nanoparticles in a layered architecture has been developed. The capillary columns were used for the separation of small molecules in hydrophilic interaction liquid chromatography mode. First, a monolith with a very large surface area of 430 m2/g was prepared by hypercrosslinking from a generic poly(4-methylstyrene-co-vinylbenzyl chloride-co-divinylbenzene) monolith via a Friedel–Crafts reaction catalyzed with iron chloride. Free radical bromination then provided this hypercrosslinked monolith with 5.7 at % Br that further reacted with cystamine under microwave irradiation, resulting in a product containing 3.8 at % sulfur. Clipping the disulfide bonds with tris(2-carboxylethyl) phosphine liberated the desired thiol groups that bind the first layer of gold nanoparticles. These immobilized nanoparticles were an intermediate ligand enabling the attachment of polyethyleneimine as a spacer followed by immobilization of the second layer of gold nanoparticles which were eventually functionalized with zwitterionic cysteine. This layered architecture, prepared using 10 nm nanoparticles, contains 17.2 wt % Au, more than twice than that found in the first layer alone. Chromatographic performance of these hydrophilic monolithic columns was demonstrated with the separation of mixtures of nucleosides and peptides in hydrophilic interaction chromatography (HILIC) mode. A column efficiency of 51 000 plates/m was achieved for retained analyte cytosine.

The isolation and characterization of mucins are critically important for obtaining insight into the molecular pathology of various diseases, including cancers and cystic fibrosis. Recently, we developed a novel membrane electrophoretic method, supported molecular matrix electrophoresis (SMME), which separates mucins on a polyvinylidene difluoride (PVDF) membrane impregnated with a hydrophilic polymer. Alcian blue staining is widely used to visualize mucopolysaccharides and acidic mucins on both blotted membranes and SMME membranes; however, this method cannot be used to stain mucins with a low acidic glycan content. Meanwhile, periodic acid–Schiff staining can selectively visualize glycoproteins, including mucins, but is incompatible with glycan analysis, which is indispensable for mucin characterizations. Here we describe a novel staining method, designated succinylation-Alcian blue staining, for visualizing mucins on a PVDF membrane. This method can visualize mucins regardless of the acidic residue content and shows a sensitivity 2-fold higher than that of Pro-Q Emerald 488, a fluorescent periodate Schiff-base stain. Furthermore, we demonstrate the compatibility of this novel staining procedure with glycan analysis using porcine gastric mucin as a model mucin.

Current desalination techniques for mass spectrometry-based protocols are problematic for performing temporal response studies where increased temporal resolution requires small samples and faster sampling frequencies, which greatly increases the number of samples and sample preparation time. These challenges are pertinent to cellular dynamics experiments, where it is important to sample the biological system frequently and with as little sample waste as possible. To address these needs, we present a dual-column online solid phase extraction (SPE) approach capable of preconcentrating and preparing a constantly perfusing sample stream, with minimal to no sample loss. This strategy is evaluated for use in microfluidic bioreactor studies specifically aimed at characterizing suitable sample flow rates, temporal resolving power, and analyte concentrations. In this work, we demonstrate that this strategy may be used for flow rates as low as 500 nL/min, with temporal resolving power on the order of 3 min, with analyte loadings ranging from femtomoles to picomoles for metabolites. Under these conditions, recoveries of ca. 80% are obtained even at femtomole loadings.

In secondary electrospray ionization (SESI) systems, gaseous analytes exposed to an elecrospray plume become ionized after charge is transferred from the charging electrosprayed particles to the sample species. Current SESI systems have shown a certain potential. However, their ionization efficiency is limited by space charge repulsion and by the high sample flows required to prevent vapor dilution. As a result, they have a poor conversion ratio of vapor into ions. We have developed and tested a new SESI configuration, termed low-flow SESI, that permits the reduction of the required sample flows. Although the ion to vapor concentration ratio is limited, the ionic flow to sample vapor flow ratio theoretically is not. The new ionizer is coupled to a planar differential mobility analyzer (DMA) and requires only 0.2 lpm of vapor sample flow to produce 3.5 lpm of ionic flow. The achieved ionization efficiency is 1/700 (one ion for every 700 molecules) for TNT and, thus, compared with previous SESI ionizers coupled with atmospheric pressure ionization-mass spectrometry (API-MS) (Mesonero, E.; Sillero, J. A.; Hernández, M.; Fernandez de la Mora, J. Philadelphia PA, 2009) has been improved by a large factor of at least 50–100 (our measurements indicate 70). The new ionizer coupled with the planar DMA and a triple quadrupole mass spectrometer (ABSciex API5000) requires only 20 fg (50 million molecules) to produce a discernible signal after mobility and MS2 analysis.

We report a method for studying membrane fusion, focusing on influenza virus fusion to lipid bilayers, which provides high temporal resolution through the rapid and coordinated initiation of individual virus fusion events. Each fusion event proceeds through a series of steps, much like multistep chemical reaction. Fusion is initiated by a rapid decrease in pH that accompanies the “uncaging” of an effector molecule from o-nitrobenzaldehyde, a photoisomerizable compound that releases a proton to the surrounding solution within microseconds of long-wave ultraviolet irradiation. In order to quantify pH values upon UV irradiation and uncaging, we introduce a simple silica nanoparticle pH sensor, useful for reporting the pH in homogeneous nanoliter volumes under conditions where traditional organic dye-type pH probes fail. Subsequent single-virion fusion events are monitored using total internal reflection fluorescence microscopy. Statistical analysis of these stochastic events uncovers kinetic information about the fusion reaction. This approach reveals that the kinetic parameters obtained from the data are sensitive to the rate at which protons are delivered to the bound viruses. Higher resolution measurements can enhance fundamental fusion studies and aid antiviral antifusogenic drug development.

Nanometer-scale pores are capable of detecting the size and concentration of nanometer-sized analytes at low concentrations upon analyzing their translocation through the pore, in small volumes and over a short time without labeling. Here, we present a simple, widely applicable, robust, and precise method to measure the zeta-potential of different nano-objects using nanopores. Zeta-potential i.e., a quantity that represents electrical charge in nanocolloids, is an important property in manufacturing of pharmaceuticals, inks, foams, cosmetics, and food. Its use is also imperative in understanding basic properties of complex dispersions including blood, living organisms, and their interaction with the environment. The characterization methods for zeta-potential are limited. Using the nanopore technique, the zeta-potential and the charge of nanoparticles can be measured independently of other parameters, such as particle size. This simple method is based on measuring the duration of the translocation of analytes through a nanopore as a function of applied voltage. A simple analytical model has been developed to extract the zeta-potential. This method is able to detect and differentiate nanometer-sized objects of similar size; it also enables the direct and precise quantitative measurement of their zeta-potential. We have applied this method to a wide range of different nanometer-sized particles and compared the results with values measured by commercially available tools. Furthermore, potential capability of this method in detection and characterization of virions is shown by measuring the low zeta-potential of HIV and EBV viruses.

Surface patterns were observed on spin-coated poly(bisphenol A decane ether) (BA-C10) films prepared with chloroform and tetrahydrofuran as the solvents. The interior structure of these surface patterns were analyzed using a time-of-flight secondary ion mass spectrometry (ToF-SIMS) equipped with a bismuth cluster source for ion imaging and a C60+ cluster source for depth profiling. For the first time, the surface patterns have been shown to be hollow rather than solid using ToF-SIMS three-dimensional (3D) analysis and optical techniques. Moreover, the microarea depth profiling analysis indicated that the hollow structure was sandwiched between two polymer layers rather than sitting on the substrate. The height of the hollow structure and the thicknesses of the polymer layers above and below the hollow structure were also estimated from the depth profiling results.

We describe a solid phase microextraction (SPME), multistep elution, transient isotachophoresis (tITP) capillary electrophoresis–tandem mass spectrometry (CE–MS/MS) procedure which employs a high sensitivity porous electrospray ionization (ESI) sprayer for the proteomic analysis of a moderately complex protein mixture. In order to improve comprehensiveness and sensitivity over a previously reported proteomic application of the ESI sprayer, we evaluated preconcentration with SPME and multistep elution prior to tITP stacking and CE separation. To maximize separation efficiency, we primarily employed electrokinetic methods for elution and separation after loading the sample by application of pressure. Conditions were developed for optimum simultaneous electrokinetic elution and sample stacking using a tryptic digest of 16 proteins to maximize peptide identifications and minimize band broadening. We performed comparative proteomic analysis of a dilution series using CE and nanoflow liquid chromatography (nLC). We found complementary peptide and protein identifications with larger quantities (100 ng) of a Pyrococcus furiosus tryptic digest, but with mass-limited amounts (5 ng) CE was 3 times more effective at identifying proteins. We attribute these gains in sensitivity to lower noise levels with the porous CE sprayer, illustrated by better signal-to-noise ratios of peptide precursor ions and associated higher XCorr values of identified peptides when compared directly to nLC. From comparative analysis of SPME-tITP-CE with direct injection CE, the SPME-tITP process improved comprehensiveness and sensitivity.

The first analytical intercomparison of fingerprint residue using equivalent samples of latent fingerprint residue and characterized by a suite of relevant techniques is presented. This work has never been undertaken, presumably due to the perishable nature of fingerprint residue, the lack of fingerprint standards, and the intradonor variability, which impacts sample reproducibility. For the first time, time-of-flight secondary ion mass spectrometry, high-energy secondary ion mass spectrometry, and X-ray photoelectron spectroscopy are used to target endogenous compounds in fingerprints and a method is presented for establishing their relative abundance in fingerprint residue. Comparison of the newer techniques with the more established gas chromatography/mass spectrometry and attenuated total reflection Fourier transform infrared spectroscopic imaging shows good agreement between the methods, with each method detecting repeatable differences between the donors, with the exception of matrix-assisted laser desorption ionization, for which quantitative analysis has not yet been established. We further comment on the sensitivity, selectivity, and practicability of each of the methods for use in future police casework or academic research.

There has been a significant increase in the use of ion mobility mass spectrometry (IM-MS) to investigate conformations of proteins and protein complexes following electrospray ionization. Investigations which employ traveling wave ion mobility mass spectrometry (TW IM-MS) instrumentation rely on the use of calibrants to convert the arrival times of ions to collision cross sections (CCS) providing “hard numbers” of use to structural biology. It is common to use nitrogen as the buffer gas in TW IM-MS instruments and to calibrate by extrapolating from CCS measured in helium via drift tube (DT) IM-MS. In this work, both DT and TW IM-MS instruments are used to investigate the effects of different drift gases (helium, neon, nitrogen, and argon) on the transport of multiply charged ions of the protein myoglobin, frequently used as a standard in TW IM-MS studies. Irrespective of the drift gas used, recorded mass spectra are found to be highly similar. In contrast, the recorded arrival time distributions and the derived CCS differ greatly. At low charge states (7 ≤ z ≤ 11) where the protein is compact, the CCS scale with the polarizability of the gas; this is also the case for higher charge states (12 ≤ z ≤ 22) where the protein is more unfolded for the heavy gases (neon, argon, and nitrogen) but not the case for helium. This is here interpreted as a different conformational landscape being sampled by the lighter gas and potentially attributable to increased field heating by helium. Under nanoelectrospray ionization (nESI) conditions, where myoglobin is sprayed from an aqueous solution buffered to pH 6.8 with 20 mM ammonium acetate, in the DT IM-MS instrument, each buffer gas can yield a different arrival time distribution (ATD) for any given charge state.

Alzheimer’s disease (AD) is the most prevalent form of dementia with an estimated worldwide prevalence of over 30 million people, and its incidence is expected to increase dramatically with an increasing elderly population. Up until now, cerebrospinal fluid (CSF) has been the preferred sample to investigate central nervous system (CNS) disorders since its composition is directly related to metabolite production in the brain. In this work, a nontargeted metabolomic approach based on capillary electrophoresis–mass spectrometry (CE–MS) is developed to examine metabolic differences in CSF samples from subjects with different cognitive status related to AD progression. To do this, CSF samples from 85 subjects were obtained from patients with (i) subjective cognitive impairment (SCI, i.e. control group), (ii) mild cognitive impairment (MCI) which remained stable after a follow-up period of 2 years, (iii) MCI which progressed to AD within a 2-year time after the initial MCI diagnostic and, (iv) diagnosed AD. A prediction model for AD progression using multivariate statistical analysis based on CE–MS metabolomics of CSF samples was obtained using 73 CSF samples. Using our model, we were able to correctly classify 97–100% of the samples in the diagnostic groups. The prediction power was confirmed in a blind small test set of 12 CSF samples, reaching a 83% of diagnostic accuracy. The obtained predictive values were higher than those reported with classical CSF AD biomarkers (Aβ42 and tau) but need to be confirmed in larger samples cohorts. Choline, dimethylarginine, arginine, valine, proline, serine, histidine, creatine, carnitine, and suberylglycine were identified as possible disease progression biomarkers. Our results suggest that CE–MS metabolomics of CSF samples can be a useful tool to predict AD progression.

This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.

Monocyte-derived macrophages play a key role in atherogenesis because their transformation into foam cells is responsible for deposition of lipids in plaques within arterial walls. The appearance of cytosolic lipid droplets is a hallmark of macrophage foam cell formation, and the molecular basics involved in this process are not well understood. Of particular interest is the intracellular fate of different individual lipid species, such as fatty acids or cholesterol. Here, we utilize Raman microscopy to image the metabolism of such lipids and to trace their subsequent storage patterns. The combination of microscopic information with Raman spectroscopy provides a powerful molecular imaging method, which allows visualization at the diffraction limit of the employed laser light and biochemical characterization through associated spectral information. In order to distinguish the molecules of interest from other naturally occurring lipids spectroscopically, deuterium labels were introduced. Intracellular distribution and metabolic changes were observed for serum albumin-complexed palmitic and oleic acid and cholesterol and quantitatively evaluated by monitoring the increase in CD scattering intensities at 0.5, 1, 3, 6, 24, 30, and 36 h. This approach may also allow for investigating the cellular trafficking of other molecules, such as nutrients, metabolites, and drugs.

The determination of nitroaromatic compounds in aqueous solution was investigated at β-cyclodextrin (β-CD)/silver nanoparticle (AgNPs) composite modified ITO electrodes. This method relies on the different reduction potentials for the various nitroaromatic isomers, the different binding strengths of the nitroaromatic isomer guests to the β-CD host, and excellent electron transfer ability of AgNPs. After incubation in a solution with different single nitroaromatic compounds, reduction peaks in the range from −550 to −913 mV were observed at the modified electrode, depending on the nitroaromatic compound present. The sensor exhibited selectivity for some isomers in a solution containing a mixture of nitroaromatic compounds. In particular, the sensor shows specificity for 4-nitroaniline and 1-chloro-2-nitrobenzene over other nitroaniline isomers and nitrochlorobenzene isomers, respectively. The results show that all the nitroaromatic compounds, 2-nitroaniline, 3-nitroaniline, 4-nitroaniline, 1-chloro-2-nitrobenzene, 1-chloro-3-nitrobenzene, and 1-chloro-4-nitrobenzene, could not only be detected but the electrode demonstrated a preference for the more strongly complexing species.

Chemical sensors based on a polymer coated quartz crystal microbalance (QCM) generally present poor molecular selectivity for compounds that contain similar functional groups and possess the same chemical properties. This paper shows for the first time that the selectivity and sensitivity of a poly(methyl methacrylate) (PMMA) based QCM sensor can be significantly enhanced for aromatic hydrocarbons by incorporating a plasticizer into the polymer film. The sensor was fabricated by spin coating PMMA onto a quartz crystal, and the influence of plasticizer type and amount on the response was evaluated. It was shown that the hydrocarbon sensitivity of plasticizer-free PMMA is negligible, while the sensitivity of plasticized PMMA was similar to or in some cases greater relative to highly responsive rubbery polymers such as polyisobutylene (PIB). Detection limits of 4.0, 1.5, 0.4, 0.6, and 0.1 ppm were obtained on a PMMA film containing 25% w/w di(2-ethylhexyl) phthalate for benzene, toluene, ethylbenzene, p-xylene, and naphthalene, respectively. We found that at low plasticizer levels (∼10% w/w) the PMMA film was more sensitive toward ethylbenzene and p-xylene over naphthalene when compared to a PIB film under similar measurement conditions. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) measurements were performed to understand the sensing mechanism, and these studies confirmed a higher hydrocarbon uptake by PMMA in the presence of plasticizer. Positron annihilation lifetime spectroscopy (PALS) studies detected variations in the free volume properties of the polymer films as a function of plasticizer content. The accessible free volume as measured by PALS was significantly less in the PMMA films compared to the PIB, and this result correlates favorably with differences in the QCM response pattern. The QCM results have been rationalized in terms of free volume theory which is responsible for the higher hydrocarbon diffusion/sorption with increased plasticizer content.

We report the development of an automated microfluidic “baby machine” to synchronize the bacterium Caulobacter crescentus on-chip and to move the synchronized populations downstream for analysis. The microfluidic device is fabricated from three layers of poly(dimethylsiloxane) and has integrated pumps and valves to control the movement of cells and media. This synchronization method decreases incubation time and media consumption and improves synchrony quality compared to the conventional plate-release technique. Synchronized populations are collected from the device at intervals as short as 10 min and at any time over four days. Flow cytometry and fluorescence cell tracking are used to determine synchrony quality, and cell populations synchronized in minimal growth medium with 0.2% glucose (M2G) and peptone yeast extract (PYE) medium contain >70% and >80% swarmer cells, respectively. Our on-chip method overcomes limitations with conventional physical separation methods that consume large volumes of media, require manual manipulations, have lengthy incubation times, are limited to one collection, and lack precise temporal control of collection times.

Two polymeric excipients, typically used in enabling drug delivery approaches, are Gelucire 44/14 (a product of Gattefosse s.a, St Priest, France) and polysorbate 80; these are known to improve solubility of poorly water-soluble drugs and, hence, increase their effective bioavailability. In addition to the use of Gelucire 44/14 and polysorbate 80 as excipients in drugs, they are also widely used as cosmetic and food additives. In general, complex structures and compositions of drug excipients impact performance of the formulation in vivo and consequently affect drug absorption. Therefore, a comparison between excipients from different suppliers and batches to batch would provide an indication of the impact on drug product performance and also the study of the effectiveness of the system and any problems associated with the formulation. In this study, high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is used to compare two different batches of Gelucire 44/14 and polysorbate 80. With the high resolving power of FTICR MS, it was possible to differentiate between batches of excipients from differences in the identified components. The improved resolution offered by FTICR MS allowed assignment of four polymeric series differences in the two batches of polysorbate 80 and the presence of one compound and three polymeric series differences in the two batches of Gelucire 44/14. The increase in the number of components assigned in the excipients batch using FTICR-MS, compared to the numbers previously assigned by lower resolution TOF MS, underlines the importance of high resolution techniques in analysis of highly complex mixtures.

In this study, laser desorption ionization (LDI) coupled to Fourier-transform ion cyclotron resonance mass spectrometry (FTICR MS) was applied to study crude oils at the molecular level. Molecular ions were the major type of ion detected by (+) mode, and deprotonated and radical anions were the major ions observed by (−) mode LDI FTICR MS. N1 and hydrocarbon classes were dominant in the class distribution plots obtained by (+) LDI FTICR MS, but other heteroatom classes, including Ox and S1, were abundant in plots obtained by (−) LDI FTICR MS. Detailed analysis of double-bond equivalence (DBE) vs carbon number plots revealed that LDI FTICR MS is more sensitive toward polyaromatic compounds than mono- or dicyclic-aromatic compounds. However, nonaromatic and aromatic O2 compounds could be detected simultaneously. An abundance of nonaromatic O2 compounds (presumably naphthenic acids) are correlated with total acid numbers, but O2 compounds with condensed structures are not. Overall, this study shows that LDI FTICR MS can be successfully used to study crude oils at the molecular level.

We have developed a novel fluorogenic nanoprobe prepared from the assembly of CdSe/ZnS quantum dot (QD) and gold (Au) nanoparticles in which QD was conjugated with a specifically designed β-secretase (BACE1) substrate peptide, which was allowed to bind to the Ni-nitrilotriacetate (Ni-NTA) modified Au nanoparticles. This coordination-mediated binding of the QD with Au nanoparticles via Ni-NTA-histidine (His) interaction resulted in highly efficient quenching of QD fluorescence through a distance-dependent fluorescence resonance energy transfer (FRET) phenomenon. The prequenched QD-Au assembly recovered the fluorescence in the presence of the BACE1 enzyme after incubation in vitro. The high quenching efficiency of AuNP and robust QD fluorescence signal recovery upon BACE1 enzymatic digestion enabled us to visualize BACE1 activity in living cells, which further allowed us to generate the half maximal inhibitory concentration (IC50) values for BACE1 inhibitors in the cell-based assay utilizing a high throughput system (HTS). These results suggest the potential application of QD-AuNP assembly toward the HTS drug screening system as a robust and efficient probe to identify active molecules in BACE1-related diseases such as Alzheimer’s disease.

We have developed a novel concept for enzymatic control of plasmonic coupling as a surface enhanced Raman scattering (SERS) nanosensor for DNA demethylation. This nanosensor is constructed by decorating gold nanoparticles (AuNPs) with Raman reporters and hemimethylated DNA probes. Demethylation of DNA probes initiates a degradation reaction of the probes by methylation-sensitive endonuclease Bsh 1236I and single-strand selective exonuclease I. This destabilizes AuNPs and mediates the aggregation of AuNPs, generating a strong plasmonic coupling SERS signal in response to DNA demethylation. This nanosensor has the advantages in its high signal-to-noise ratio, superb specificity, and rapid, convenient, and reproducible detection with homogeneous, single-step operation. Thus, it provides a useful platform for detecting DNA demethylation and related molecular diagnostics and drug screening. This work is the first time that enzymatic degradation of DNA substrate probes has been utilized to induce aggregation of AuNPs such that reproducible, sensitive SERS signals can be achieved from biological recognition events. This enzymatic control mechanism for plasmonic coupling may create a new paradigm for the development of SERS nanosensors.

Here, we describe a method for the comparative analysis of ribonucleic acids (RNAs). This method allows sequence or modification information from a previously uncharacterized RNA to be obtained by direct comparison with a reference RNA, whose sequence or modification information is known. This simple and rapid method is enabled by the differential labeling of two RNA samples. One sample, the reference RNA, is labeled with 16O during enzymatic digestion. The second sample, the candidate or unknown RNA, is labeled with 18O. By combining the two digests, digestion products that share the same sequence or post-transcriptional modification(s) between the reference and candidate will appear as doublets separated by 2 Da. Sequence or modification differences between the two will generate singlets that can be further characterized to identify how the candidate sequence differs from the reference. We illustrate the application of this approach for sequencing individual RNAs and demonstrate how this method can be used to identify sequence-specific differences in RNA modification. This comparative analysis of RNA digests (CARD) approach is scalable to multiple candidate RNAs using one or multiple reference RNAs and is compatible with existing methods for quantitative analysis of RNAs.

HIV-1 integrase strand transfer inhibitors are an important class of compounds targeted for the treatment of HIV-1 infection. Microdosing has emerged as an attractive tool to assist in drug candidate screening for clinical development, but necessitates extremely sensitive bioanalytical assays, typically in the pg/mL concentration range. Currently, accelerator mass spectrometry is the predominant tool for microdosing support, which requires a specialized facility and synthesis of radiolabeled compounds. There have been few studies attempted to comprehensively assess a liquid chromatography–tandem mass spectrometry (LC–MS/MS) approach in the context of microdosing applications. Herein, we describe the development of automated LC–MS/MS methods to quantify five integrase inhibitors in plasma with the limits of quantification at 1 pg/mL for raltegravir and 2 pg/mL for four proprietary compounds. The assays involved double extractions followed by UPLC coupled with negative ion electrospray MS/MS analysis. All methods were fully validated to the rigor of regulated bioanalysis requirements, with intraday precision between 1.20 and 14.1% and accuracy between 93.8 and 107% at the standard curve concentration range. These methods were successfully applied to a human microdose study and demonstrated to be accurate, reproducible, and cost-effective. Results of the study indicate that raltegravir displayed linear pharmacokinetics between a microdose and a pharmacologically active dose.

In this aritcle, we have developed an interesting imaging method for intracellular ATP molecules with semiquantitation. While there has been a lot of work in understanding intracellular events, very few can come close to quantitation or semiquantitation in living cells. In this work, we made an effective use of nanomaterials, graphene oxides, both as a quencher and a carrier for intracellular delivery. In addition, this graphene oxide also serves as the carrier for reference probes for fluorescent imaging. An ATP aptamer molecular beacon (AAMB) is adsorbed on graphene oxide (GO) to form a double quenching platform. The AAMB/GO spontaneously enters cells, and then AAMB is released and opened by intracellular ATP. The resulting fluorescence recovery is used to perform ATP live-cell imaging with greatly improved background and signaling. Moreover, a control ssDNA, which is released nonspecifically from GO by nontarget cellular proteins, can serve as an internal reference for ATP semiquantification inside living cells using the intensity ratio of the AAMB and control. This approach can serve as a way for intracellular delivery and quantitative analysis.

A quantitative multianalyte immunoassay utilizing luminescent upconverting single-crystal nanoparticles as reporters on an antibody array-in-well platform was demonstrated. Upconverting nanoparticles are inorganic rare earth doped materials that have the unique feature of converting low energy infrared radiation into higher energy visible light. Autofluorescence, commonly limiting the sensitivity of fluorescence-based assays, can be completely eliminated with photon upconversion technology because the phenomenon does not occur in biological materials. Biotinylated antibodies for three analytes (prostate specific antigen, thyroid stimulating hormone, and luteinizing hormone) were printed in an array format onto the bottom of streptavidin-coated microtiter wells. Analyte dilutions were added to the wells, and the analytes were detected with antibody-coated upconverting nanoparticles. Binding of the upconverting nanoparticles was imaged with an anti-Stokes photoluminescence microwell imager, and the standard curves for each analyte were quantified from the selected spot areas of the images. Single analyte and reference assays were also carried out to compare with the results of the multianalyte assay. Multiplexing did not have an effect on the assay performance. This study demonstrates the feasibility of upconverting single-crystal nanoparticles for imaging-based detection of quantitative multianalyte assays.

The percentage of glycosylated hemoglobin A1c (%GHbA1c) in human whole blood indicates the average plasma glucose concentration over a prolonged period of time and is used to diagnose diabetes. However, detecting GHbA1c in the whole blood using immunoassays has limited detection sensitivity due to its low percentage in total hemoglobin (tHb) and interference from various glycan moieties in the sample. We have developed a sandwich immunoassay using an antibody microarray on a polydimethylsiloxane (PDMS) substrate modified with fluorinated compounds to detect tHb and glycosylated hemoglobin A1c (GHbA1c) in human whole blood without sample pretreatment. A polyclonal antibody against hemoglobin (Hb) immobilized on PDMS is used as a common capture probe to enrich all forms of Hb followed by detection via monoclonal anti-Hb and specific monoclonal anti-GHbA1c antibodies for tHb and GHbA1c detection, respectively. This method prevents the use of glycan binding molecules and dramatically reduces the background interference, yielding a detection limit of 3.58 ng/mL for tHb and 0.20 ng/mL for GHbA1c. The fluorinated modification on PDMS is superior to the glass substrate and eliminates the need for the blocking step which is required in commercial enzyme linked immunosorbent assay (ELISA) kits. Moreover, the detection sensitivity for GHbA1c is 4–5 orders of magnitude higher, but the required sample amount is 25 times less than the commercial method. On the basis of patient sample data, a good linear correlation between %GHbA1c values determined by our method and the certified high performance liquid chromatography (HPLC) standard method is shown with R2 > 0.98, indicating the great promise of the developed method for clinical applications.

Direct analysis in real time (DART) ionization method is used with a time-of-flight (TOF) mass spectrometer to perform the analysis of industrial polyethylene pellets free of additives or containing Irgafos 168 as stabilizing agent without any sampling step. The developed analytical method uses the [M + H]+ ion of the bis(2-ethylhexyl) phthalate (DEHP) for performing the exact mass measurements of the stabilizer and polymer ions using the mass drift compensation procedure available on the AccuTOF mass spectrometer. DEHP is in fact a plastic contaminant always presents on the mass spectra of the analyzed samples. The mass spectra allow one to characterize either the ions of the polyethylene and that of the Irgafos. The analysis of thermally treated samples show that the polymer does not undergo any degradation when the Irgafos is present in the bulk of the material, and the role played by the Irgafos 168 is that of an oxygen trapping agent. Under UV exposure, the DART-TOF MS analyses performed on the exposed polyethylene pellets shows that the Irgafos 168 behavior toward the UV radiations is different since this one reacts by cleavages of its P–O bonds to prevent the degradation of the polymer. These interpretations are supported by all the elemental formula determination of the detected ions.

Plasma membrane derived vesicles are used as a model system for the biochemical and biophysical investigations of membrane proteins and membrane organization. The most widely used vesiculation procedure relies on formaldehyde and dithiothreitol (DTT), but these active chemicals may introduce artifacts in the experimental results. Here we describe a procedure to vesiculate Chinese hamster ovary (CHO) cells, widely used for the expression of recombinant proteins, using a hypertonic vesiculation buffer containing chloride salts and no formaldehyde or DTT. We characterize the size distribution of the produced vesicles. We also show that these vesicles can be used for the biophysical characterization of interactions between membrane proteins.

We present a highly sensitive metal enhanced fluorescence (MEF) method based on a novel silver nanostructure fabricated with Cy5-functionalized silver nanoparticles (AgNPs) and AgNO3. The analytical performance has been demonstrated by microarray detection of streptavidin (SA) and human IgE. The fluorescence intensity can be enhanced substantially with the combined use of AgNPs and fluorescence enhanced solution (FES). Aptamers have been used for the preparation of Tag-C, which demonstrate IgE detection from 0.5 ng/mL to 16 ng/mL, and the limit of detection is determined to be 0.25 ng/mL. SEM images show nanogaps exist in the aggregated silver nanoparticles and the nanogaps allow for the trap of fluorophores in the nanostructures that emit brighter light upon excitation. The silver nanostructures formed by Tags and FES proved to be an excellent platform for MEF of fluorophores whose excitation and emission occurred between 436 nm and 1000 nm. Finite-difference time-domain (FDTD) simulation has been carried out to confirm the enhanced electromagnetic field inside silver nanostructures, leading to strong overlap/resonance coupling and eventual fluorescence enhancement.

A major bottleneck in high-throughput protein production is the validation step, which is why parallel and automated sample processing methods are highly desirable. Also, a miniaturized sample preparation format is preferred, as the reduction of reagent volumes significantly decreases the analysis cost per sample. We have developed an automated and miniaturized protein sequence verification protocol for recombinant proteins utilizing peptide mass fingerprinting and MS/MS analysis. The integrated selective enrichment target (ISET) platform, previously developed in our group, with its dual functionality, being both a sample preparation platform and a MALDI target plate, is employed. All steps including immobilized metal ion affinity chromatography of protein on cobalt-loaded beads, tryptic digestion, and MALDI MS analysis are performed in an array format, without any sample transfers, on the same ISET chip. The automated configuration reduced the sample preparation time significantly. Starting with crude lysate, a full plate of 48 purified, digested samples prepared for MALDI-MS can be generated in 4 h, with only 30 min of operator involvement. This paper demonstrates the utility of the method by parallel analysis of 45 His-tagged human recombinant proteins.

A simple, sensitive, and label-free method for microRNA (miRNA) biosensing was described using oligonucleotide encapsulated silver nanoclusters (Ag-NCs) as effective electrochemical probes. The functional oligonucleotide probe integrates both recognition sequence for hybridization and template sequence for in situ synthesis of Ag-NCs, which appears to possess exceptional metal mimic enzyme properties for catalyzing H2O2 reduction. The miRNA assay employs gold electrodes to immobilize the molecular beacon (MB) probe. After the MB probe subsequently hybridizes with the target and functional probe, the oligonucleotide encapsulated Ag-NCs are brought to the electrode surface and produce a detection signal, in response to H2O2 reduction. An electrochemical miRNA biosensor down to 67 fM with a linear range of 5 orders of magnitude was obtained. Meanwhile, the MB probe allows the biosensor to detect the target with high selectivity. The Ag-NCs-based approach provides a novel avenue to detect miRNA with high sensitivity and selectivity while avoiding laborious label and signal amplification. It is convinced that rational introduction of signal amplification strategy to the Ag-NCs-based bioanalysis can further improve the sensitivity. To our best knowledge, this is the first application of the electrocatalytic activity of Ag-NCs in bioanalysis, which would be attractive for genetic analysis and clinic biomedical application.

We have developed a multistep strategy that integrates data from several large-scale experiments that suffer from systematic between-experiment variation. This strategy removes such variation that would otherwise mask differences of interest. It was applied to the evaluation of wood chemical analysis of 736 hybrid aspen trees: wild-type controls and transgenic trees potentially involved in wood formation. The trees were grown in four different greenhouse experiments imposing significant variation between experiments. Pyrolysis coupled to gas chromatography/mass spectrometry (Py-GC/MS) was used as a high throughput-screening platform for fingerprinting of wood chemotype. Our proposed strategy includes quality control, outlier detection, gene specific classification, and consensus analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) method was used to generate the consensus chemotype profiles for each transgenic line. These were thereafter compiled to generate a global dataset. Multivariate analysis and cluster analysis techniques revealed a drastic reduction in between-experiment variation that enabled a global analysis of all transgenic lines from the four independent experiments. Information from in-depth analysis of specific transgenic lines and independent peak identification validated our proposed strategy.

Collection of biological fluids on clinical filter papers shows important advantages from a logistic point of view, although analysis of these specimens is far from straightforward. Concerning urine analysis, and particularly when direct trace elemental analysis by laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS) is aimed at, several problems arise, such as lack of sensitivity or different distribution of the analytes on the filter paper, rendering obtaining reliable quantitative results quite difficult. In this paper, a novel approach for urine collection is proposed, which circumvents many of these problems. This methodology consists on the use of precut filter paper discs where large amounts of sample can be retained upon a single deposition. This provides higher amounts of the target analytes and, thus, sufficient sensitivity, and allows addition of an adequate internal standard at the clinical lab prior to analysis, therefore making it suitable for a strategy based on unsupervised sample collection and ulterior analysis at referral centers. On the basis of this sampling methodology, an analytical method was developed for the direct determination of several elements in urine (Be, Bi, Cd, Co, Cu, Ni, Sb, Sn, Tl, Pb, and V) at the low μg L–1 level by means of LA-ICPMS. The method developed provides good results in terms of accuracy and LODs (≤1 μg L–1 for most of the analytes tested), with a precision in the range of 15%, fit-for-purpose for clinical control analysis.

Several recent deaths in the U.K. have been attributed to “legal high” drugs and in particular to (±)-4-methylmethcathinone ((±)-mephedrone). Recent literature has begun to focus on the chemical analysis of mephedrone and related substituted cathinones and methcathinones; however, no studies involving the application of stable isotope analysis to these compounds has yet emerged. Such studies have, for example, the potential to provide information linking the final products to a particular precursor by the manufacturer. In this study, the use of stable isotope profiling was explored to provide a possible connection between product and precursor chemicals. Six samples each of mephedrone were prepared using precursor chemicals from two different manufacturers, providing 12 samples in total. Synthesis was via a stable intermediate

A new equation is derived for estimating the sensitivity when the multivariate curve resolution-alternating least-squares (MCR-ALS) method is applied to second-order multivariate calibration data. The validity of the expression is substantiated by extensive Monte Carlo noise addition simulations. The multivariate selectivity can be derived from the new sensitivity expression. Other important figures of merit, such as limit of detection, limit of quantitation, and concentration uncertainty of MCR-ALS quantitative estimations can be easily estimated from the proposed sensitivity expression and the instrumental noise. An experimental example involving the determination of an analyte in the presence of uncalibrated interfering agents is described in detail, involving second-order time-decaying sensitized lanthanide luminescence excitation spectra. The estimated figures of merit are reasonably correlated with the analytical features of the analyzed experimental system.

Spinal cord injury triggers a series of complex biochemical alterations of nervous tissue. Up to now, such cellular events could not be studied without conventional tissue staining. The development of optical, label-free imaging techniques could provide powerful monitoring tools with the potential to be applied in vivo. In this work, we assess the ability of vibrational spectroscopy to generate contrast at molecular level between normal and altered regions in a rat model of spinal cord injury. Using tissue sections, we demonstrate that Fourier transform infrared (FT-IR) spectroscopy and spontaneous Raman spectroscopy are able to identify the lesion, the surrounding scar, and unharmed normal tissue, delivering insight into the biochemical events induced by the injury and allowing mapping of tissue degeneration. The FT-IR and Raman spectroscopic imaging provides the basis for fast multimodal nonlinear optical microscopy (coherent anti-Stokes Raman scattering, endogenous two-photon fluorescence, and second harmonic generation). The latter proves to be a fast tool for imaging of the lesion on unstained tissue samples, based on the alteration in lipid content, extracellular matrix composition, and microglia/macrophages distribution pattern. The results establish these technologies in the field of regeneration in central nervous system, with the long-term goal to extend them to intravital use, where fast and nonharmful imaging is required.

We report the shotgun proteomic analysis of mammalian cell lysates that contain low nanogram amounts of protein. Proteins were denatured using methanol, digested using immobilized trypsin, and analyzed by UPLC-ESI-MS/MS. The approach generated more peptides and higher sequence coverage for a mixture of three standard proteins than the use of free trypsin solution digestion of heat- or urea-denatured proteins. We prepared triplicate RAW 264.7 cell lysates that contained 6, 30, 120, and 300 ng of protein. An average of 2 ± 1, 23 ± 2, 134 ± 11, and 218 ± 26 proteins were detected for each sample size, respectively. The numbers of both protein and peptide IDs scaled linearly with the amount of sample taken for analysis. Our approach also outperformed traditional methods (free trypsin digestion of heat- or urea-denatured proteins) for 6–300 ng RAW 264.7 cell protein analysis in terms of number of peptides and proteins identified. The use of accurate mass and time (AMT) tags resulted in the identification of an additional 16 proteins based on 20 peptides from the 6 ng cell lysate prepared with our approach. When AMT analysis was performed for the 6 ng cell lysate prepared with traditional methods, no reasonable peptide signal could be obtained. In all cases, roughly ∼30% of the digested sample was taken for analysis, corresponding to the analysis of a 2 ng aliquot of homogenate from the 6 ng cell lysate.

In two-dimensional chromatography, the orthogonality of separation is important for achieving high peak capacity. In this paper, a number of different metrics are compared as measures of orthogonality. Six peptide elution data sets acquired on different stationary phases are plotted against reversed phase retention data and examined as two-dimensional chromatographic pairs. The data, including six in silico prepared data pairs, are utilized to challenge and compare selected orthogonality metrics. The metrics include correlation coefficients, mutual information, box-counting dimensionality, and surface fractional coverage with different hulls. Although correlation coefficients were found to be less suited for the intended purpose, other methods can provide a suitable measure of orthogonality. The presented results are discussed in terms of method utility, simplicity, and applicability for statistically small sets of chromatographic data. Two of the methods, box counting dimensionality and fractional coverage, were found to be mathematically related.

The determination of the carbon concentration of single-wall carbon nanotubes (SWCNTs) in a given dispersion is a basic requirement for many studies. The commonly used optical absorption-based concentration measurement is complicated by the spectral change due to variations in nanotube chirality and length. In particular, the origin of the observed length-dependent spectral change and its effect on concentration determination has been the subject of considerable debate. Here, we use length-fractionated DNA-wrapped SWCNTs to establish the relationship between SWCNT carbon concentration and optical absorption spectra by directly quantifying the amount of wrapping DNA and, independently, the DNA/carbon nanotube mass ratio. We find that SWCNT carbon concentrations derived from either the E11 peak or spectral baseline deviate significantly from the SWCNT carbon concentrations derived from the DNA measurement method. Instead, SWCNT carbon concentrations derived from the spectral integration of the E11 optical transition region match most closely with the DNA-derived SWCNT carbon concentrations. We also observe that shorter SWCNT fractions contain more curved carbon nanotubes, and propose that these defective nanotubes are largely responsible for the observed spectral variation with nanotube length.

In designing a protein electrophoresis platform composed of a single-inlet, single-outlet microchannel powered solely by voltage control (no pumps, values, injectors), we adapted the original protein electrophoresis format—moving boundary electrophoresis (MBE)—to a high-performance, compact microfluidic format. Key to the microfluidic adaptation is minimization of injection dispersion during sample injection. To reduce injection dispersion, we utilize a photopatterned free-solution–polyacrylamide gel (PAG) stacking interface at the head of the MBE microchannel. The nanoporous PAG molecular sieve physically induces a mobility shift that acts to enrich and sharpen protein fronts as proteins enter the microchannel. Various PAG configurations are characterized, with injection dispersion reduced by up to 85%. When employed for analysis of a model protein sample, microfluidic PAG MBE baseline-resolved species in 5 s and in a separation distance of less than 1 mm. PAG MBE thus demonstrates electrophoretic assays with minimal interfacing and sample handling, while maintaining separation performance. Owing to the short separation lengths needed in PAG MBE, we reduced the separation channel length to demonstrate an electrophoretic immunoassay powered with an off-the-shelf 9 V battery. The electrophoretic immunoassay consumed less than 3 μW of power and was completed in 30 s. To our knowledge, this is the lowest voltage and lowest power electrophoretic protein separation reported. Looking forward, we see the low-power PAG MBE as a basis for highly multiplexed protein separations (mobility shift screening assays) as well as for portable low-power diagnostic assays.

The development of hypoxic areas often takes place in solid tumors and leads cells to undergo adaptive signalization like autophagy. This process is responsible for misfolded or aggregated proteins and nonfunctional organelle recycling, allowing cells to maintain their energetic status. However, it could constitute a double-edged pathway leading to both survival and cell death. So, in response to stress such as hypoxia, autophagic and apoptotic cells are often mixed. To specifically study and characterize autophagic cells and the process, we needed to develop a method able to (1) isolate autophagic subpopulation and (2) respect apoptotic and autophagic status. Sedimentation field-flow fractionation (SdFFF) was first used to monitor physical parameter changes due to the hypoxia mimetic CoCl2 in the p53 mutated SKNBE2(c) human neuroblastoma cell line. Second, we showed that “hyperlayer” elution is able to prepare autophagic enriched populations, fraction (F3), overexpressing autophagic markers (i.e., LC3-II accumulation and punctiform organization of autophagosomes as well as cathepsin B overactivity). Conversely, the first eluted fraction exhibited apoptotic markers (caspase-3 activity and Bax increased expression). For the first time, SdFFF was employed as an analytical tool in order to discriminate apoptotic and autophagic cells, thus providing an enriched autophagic fraction consecutively to a hypoxic stress.

O-Acetylated N-glycans from fish serum of Atlantic salmon (Salmo salar) are characterized by capillary electrophoresis (CE) in conjunction with both laser-induced fluorescence (LIF) and mass spectrometry (MS) detection methods. Glycans derivatized with negatively charged fluorescent label 8-aminopyrene-1,2,6-trisulfonate (APTS) were separated to obtain a CE-LIF profile of the complex glycan mixture, and the profile concurs with that obtained by using electrospray mass spectrometry. The identity of the APTS-labeled glycans was confirmed by CE–MS. The same glycans can be identified also in their native state by CE–MS without derivatization. The structural variations of O-acetylated sialic acid isomers in fish serum glycans are investigated by CE–MS/MS. Selected ion monitoring provided useful structural information of the underivatized glycans from fragmentation spectra. New complex fish serum glycans that are not reported previously were observed and characterized. These methods may be useful not only for the characterization of acetylation of complex glycans but also to study other types of glycan modifications, as well as to allow determination of overall glycan composition in glycoproteins.

Lipocalin-2 (Lcn2) is a biomarker for many inflammatory-based diseases, including acute kidney injury, cardiovascular stress, diabetes, and various cancers. Inflammatory transitions occur rapidly in kidney and cardiovascular disease, for which an in-line monitor could be beneficial. Microcantilever devices with aptamers as recognition elements can be effective and rapidly responsive sensors. Here, we have selected and characterized an RNA aptamer that specifically binds mouse Lcn2 (mLcn2) with a dissociation constant of 340 ± 70 nM in solution and 38 ± 22 nM when immobilized on a surface. The higher apparent affinity of the immobilized aptamer may result from its effective multivalency that decreases the off-rate. The aptamer competes with a catechol iron-siderophore, the natural ligand of mLcn2. This and the results of studies with mLcn2 mutants demonstrate that the aptamer binds to the siderophore binding pocket of the protein. A differential interferometer-based microcantilever sensor was developed with the aptamer as the recognition element in which the differential response between two adjacent cantilevers (a sensing/reference pair) is utilized to detect the binding between mLcn2 and the aptamer, ensuring that sensor response is independent of environmental influences, distance between sensing surface and detector and nonspecific binding. The system showed a detection limit of 4 nM. This novel microcantilever aptasensor has potential for development as an in-line monitoring system for mLcn2 in studies of animal models of acute diseases such as kidney and cardiac failure.

Laser ablation inductively coupled plasma mass spectrometry has been applied to determine the thickness of subnanometer (subnm) metallic layers. Metallic Nd was deposited onto Si wafers with 0.5, 1, 3, and 6 nm thickness and covered by a 10 nm Al coating. Integrated ion signals corresponded to the layer thickness, indicating that external calibration provides accurate data. Utilizing sensitivity ratios obtained from ablation of a glass standard reference material (SRM) and the Al layer as reference, the deviations between prepared and measured layer thickness were less than 10%. A further attempt was made to determine the layer thickness with the absolute sensitivity obtained from ablation of a glass SRM. The approach also yielded a linear correlation between determined and actual layer thickness, but bias and interday variability were significantly higher. This is assumed to result from imprecise determination of the crater size when ablating the glass SRM. This study shows that subnm layers of metals can be analyzed for their thickness either using reference materials of identical composition or using sensitivity ratios when one layer can be used as a reference. Absolute determination of the layer thickness is less accurate but can circumvent the lack of reference materials of similar composition.

During the development of new materials demonstrating biological activity, prediction and identification of reactive intermediates generated in the course of drug metabolism in the human liver is of great importance. We present a rapid and purely instrumental method for the structure elucidation of possible phase I metabolites. With electrochemical (EC) conversion adopting the oxidative function of liver-inherent enzymes and nuclear magnetic resonance (NMR) spectroscopy enabling structure elucidation, comprehensive knowledge on potential metabolites can be gained. Paracetamol (APAP) has been known to induce hepatotoxicity when exceeding therapeutic doses and was therefore selected as the test compound. The reactive metabolite N-acetyl-p-benzoquinone imine has long been proven to be responsible for the toxic side effects of APAP and can easily be generated by EC. EC coupled online to NMR is a straightforward technique for structure elucidation of reactive drug intermediates at an early stage in drug discovery.

Samples of 10 μL of whole blood containing citalopram, loperamide, methadone, and sertraline as model substances were spotted on alginate and chitosan foams as sampling media. After drying and storage at room temperature, the punched out dried blood spot and the foam was dissolved in 300 μL of 1 mM HCl. With alginate foam as sampling medium, the analytes dissolved completely after 3 min. Enrichment and cleanup was performed with electromembrane extraction for 10 min. The analytes were collected in 21 μL of 10 mM formic acid as the acceptor phase, and the extracts were analyzed by liquid chromatography–mass spectrometry (LC–MS). Sample preparation of blood spots on commercial cards was also performed (Whatman FTA DMPK and Agilent Bond Elut DMS) using elution procedures recommended by the manufacturers. The recoveries obtained with the commercial cards were lower for most of the model analytes compared to the recoveries obtained with alginate and chitosan foams as sampling media. The procedure used for Agilent Bond Elut DMS showed higher recoveries than the procedure used for Whatman FTA DMPK-A, but the time needed for sample preparation was significantly longer (nearly 2 h). The stability of the model substances on the alginate foam was acceptable within 50 days of storage. The limit of quantification (LOQ) defined as S/N = 10, was 1.2, 5.5, 2.0, and 5.3 ng/mL for citalopram, loperamide, methadone, and sertraline, respectively. Linear calibration graphs were obtained in the range 17.5–560 ng/mL with r2 values 0.983–0.995, and the relative standard deviations were below 20%.

A novel online enzyme reactor incorporating peptide-N-glycosidase F (PNGase F) on a monolithic polymer support has been developed to allow the rapid simultaneous release of both neutral and acidic N-linked glycans from glycoproteins. The PNGase F monolithic reactor was fabricated in a fused silica using glycidyl methacrylate-co-ethylene dimethacrylate polymer. The reactor was coupled to a C8 trap and a porous graphitic carbon (PGC) HPLC-chip. This arrangement was interfaced to an ion trap mass spectrometer for liquid chromatography–mass spectrometry (LC–MS) and liquid chromatography–tandem mass spectrometry (LC–MS/MS) analyses. The performance of the PNGase F reactor was optimized using the MS signal for the disialylated biantennary N-glycan derived from fetuin. Optimum conditions for glycan release were attained at room temperature using a loading flow rate of 2 μL/min and a reaction time of 6 min. The loading capacity of the reactor was determined to be around 2 pmol of glycoprotein. The online digestion and MS characterization experiments resulted in sensitivities as high as 100 fmol of glycoprotein and 0.1 μL of human blood serum. The enzyme reactor activity was also shown to remain stable after 1 month of continuous use. Both small and large glycoproteins as well as glycoproteins containing high-mannose glycans, fucolsylated glycans, sialylated glycans, and hybrid structures were studied. The model glycoproteins included ribonuclease B, fetuin, α1-acid glycoprotein, immunoglobulin, and thyroglobulin. All N-glycans associated with these model glycoproteins were detected using the online PNGase F reactor setup.

Here we report the theory and experimental study of the steady-state voltammetric behavior of a microelectrode used as a limiting pole in a closed bipolar electrochemical cell. We show that the steady-state voltammetric response of a microelectrode used in a closed bipolar cell can be quantitatively understood by considering the responses of both poles in their respective conventional two-electrode setups. In comparison to a conventional electrochemical cell, the voltammetric response of the bipolar cell has a similar sigmoidal shape and limiting current; however, the response is often slower than that of the typical two-electrode setup. This leads to a broader voltammogram and a decreased wave slope, which can be somewhat misleading, causing the appearance that the process being studied is irreversible when it instead can be a result of the coupling of two reversible processes. We show that a large limiting current on the excess pole would facilitate the observation of a faster voltammetric response and that both redox concentration and electrode area of the excess pole affect the wave shape. Both factors should be maximized in electroanalytical experiments in order to obtain fast voltammetric responses on the main electrode of interest and to detect quick changes in analyte concentrations.

We introduce a new format for particle-based immunoassays relying on digital microfluidics (DMF) and magnetic forces to separate and resuspend antibody-coated paramagnetic particles. In DMF, fluids are electrostatically controlled as discrete droplets (picoliters to microliters) on an array of insulated electrodes. By applying appropriate sequences of potentials to these electrodes, multiple droplets can be manipulated simultaneously and various droplet operations can be achieved using the same device design. This flexibility makes DMF well-suited for applications that require complex, multistep protocols such as immunoassays. Here, we report the first particle-based immunoassay on DMF without the aid of oil carrier fluid to enable droplet movement (i.e., droplets are surrounded by air instead of oil). This new format allowed the realization of a novel on-chip particle separation and resuspension method capable of removing greater than 90% of unbound reagents in one step. Using this technique, we developed methods for noncompetitive and competitive immunoassays, using thyroid stimulating hormone (TSH) and 17β-estradiol (E2) as model analytes, respectively. We show that, compared to conventional methods, the new DMF approach reported here reduced reagent volumes and analysis time by 100-fold and 10-fold, respectively, while retaining a level of analytical performance required for clinical screening. Thus, we propose that the new technique has great potential for eventual use in a fast, low-waste, and inexpensive instrument for the quantitative analysis of proteins and small molecules in low sample volumes.

Ion-selective membranes based on porous polypropylene membranes doped with an ionophore and a lipophilic cation-exchanger are used here in a new tandem measurement mode that combines dynamic electrochemistry and zero current potentiometry into a single protocol. Open circuit potential measurements yield near-Nernstian response slopes in complete analogy to established ion-selective electrode methodology. Such measurements are well established to give direct information on the so-called free ion concentration (strictly, activity) in the sample. The same membrane is here also operated in a constant current mode, in which the localized ion depletion at a transition time is visualized by chronopotentiometry. This dynamic electrochemistry methodology gives information on the labile ion concentration in the sample. The sequential protocol is established on potassium and calcium ion-selective membranes. An increase of the ionophore concentration in the membrane to 180 mM makes it possible to determine calcium concentrations as high as 3 mM by chronopotentiometry, thereby making it possible to directly detect total calcium in undiluted blood samples. Recovery times after current perturbation depend on the current amplitude but can be kept to below 1 min for the polypropylene based ion-selective membranes studied here. Plasticized PVC as membrane material is less suited for this protocol, especially when the measurement at elevated concentrations is desired. An analysis of current amplitudes, transition times, and concentrations shows that the data are described by the Sand equation and that migration effects are insignificant. A numerical model describes the experimental findings with good agreement and gives guidance on the required selectivity in order to observe a well-resolved transition time and on the expected errors due to insufficient selectivity. The simulations suggest that the methodology compares well to that of open circuit potentiometry, despite giving complementary information about the sample. The tandem methodology is demonstrated in a titration of calcium with nitrilotriacetic acid (NTA) and in the direct detection of calcium in undiluted heparinized and citrated blood.

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

We report the fabrication of two different cell patterns based on negative dielectrophoresis (n-DEP) and apply it to simple and rapid distinction of cells with specific surface antigens from a cell population. The DEP device for cell manipulation comprised a microfluidic channel with an upper indium tin oxide (ITO) electrode and a lower ITO-interdigitated band array (ITO–IDA) electrode modified with an antibody. Cells immediately accumulated on the surface in the gap area between both bands of the ITO–IDA electrode by n-DEP upon AC voltage between the upper ITO and both lower bands. Switching of the applied band electrode voltage resulted in the removal of accumulated cells to form another pattern because of the formation of a different electric field pattern in the device. Modifying the ITO–IDA surface with the antibody inhibited the removal of the cells with a specific surface antigen for irreversible capture by immunoreactions during the first accumulation. In this study, we targeted the CD33 surface antigen expressed on human promyelocytic leukemia cells (HL-60). The time required for the assay was substantially short: 60 s for forcing and 60 s for separating the unbound cells. Furthermore, the present method does not require pretreatment such as target labeling or washing of unbound cells. Moreover, the use of the swing technique considerably improved cell binding to the antibody-modified surface for cells with a specific surface antigen. The distinct integration of cells with n-DEP in the high conductivity medium provided higher cell binding efficiency compared to that obtained in our previous study (Hatanaka, H.; Yasukawa, T.; Mizutani, F. Anal. Chem., 2011, 83, 7207–7212) without loss of rapidity and simplicity.

Biofouling and tissue inflammation present major challenges toward the realization of long-term implantable glucose sensors. Following sensor implantation, proteins and cells adsorb on sensor surfaces to not only inhibit glucose flux but also signal a cascade of inflammatory events that eventually lead to permeability-reducing fibrotic encapsulation. The use of drug-eluting hydrogels as outer sensor coatings has shown considerable promise to mitigate these problems via the localized delivery of tissue response modifiers to suppress inflammation and fibrosis, along with reducing protein and cell absorption. Biodegradable poly (lactic-co-glycolic) acid (PLGA) microspheres, encapsulated within a poly (vinyl alcohol) (PVA) hydrogel matrix, present a model coating where the localized delivery of the potent anti-inflammatory drug dexamethasone has been shown to suppress inflammation over a period of 1–3 months. Here, it is shown that the degradation of the PLGA microspheres provides an auxiliary venue to offset the negative effects of protein adsorption. This was realized by: (1) the creation of fresh porosity within the PVA hydrogel following microsphere degradation (which is sustained until the complete microsphere degradation) and (2) rigidification of the PVA hydrogel to prevent its complete collapse onto the newly created void space. Incubation of the coated sensors in phosphate buffered saline (PBS) led to a monotonic increase in glucose permeability (50%), with a corresponding enhancement in sensor sensitivity over a 1 month period. Incubation in serum resulted in biofouling and consequent clogging of the hydrogel microporosity. This, however, was partially offset by the generated macroscopic porosity following microsphere degradation. As a result of this, a 2-fold recovery in sensor sensitivity for devices with microsphere/hydrogel composite coatings was observed as opposed to similar devices with blank hydrogel coatings. These findings suggest that the use of macroscopic porosity can reduce sensitivity drifts resulting from biofouling, and this can be achieved synergistically with current efforts to mitigate negative tissue responses through localized and sustained drug delivery.

Evaluation of plasma renin activity is essential to the assessment of renin-related diseases such as hypertension, congestive heart failure, and cancers. Here, we develop a single quantum dot (QD) based nanosensor for sensitive detection of renin activity. This single-QD-based nanosensor consists of a streptavidin-coated QD and multiple biotinylated and Cy5-labeled peptide substrates, which form a QD/substrate/Cy5 complex where fluorescence resonance energy transfer (FRET) occurs with the QD as the donor and Cy5 as the acceptor. The presence of renin leads to the cleavage of the substrate and the separation of Cy5 from the QD and consequently the decrease of FRET efficiency and the reduction of Cy5 counts. Through the measurement of Cy5 counts by total internal reflection fluorescence (TIRF) microscopy, the renin activity can be quantitatively evaluated at the single-molecule level. This single-QD-based nanosensor can measure not only the renin concentration, but also the enzymatic velocity and the Michaelis–Menten kinetic parameters, and has significant advantages of simplicity, low cost with minimum sample consumption, and high sensitivity with a detection limit of 25 pM. This single-QD-based nanosensor might be further applied to monitor a variety of important enzymatic biomarkers such as kinases and endonuleases.

Protein expression analysis is one of the most powerful tools to further the understanding of biological systems. Progress in the field of mass spectrometry has shifted focus from gel-based approaches to the upcoming LC-selected reaction monitoring (SRM) technique which combines high technical accuracy with absolute quantification of proteins and the capability for high-throughput analyses. Due to these properties, LC-SRM has the potential to become the foundation for biomarker analysis, targeted hypothesis driven proteomic studies and contribute to the field of systems biology. While the performance of LC-SRM applied to samples from various bodily fluids, particularly plasma, and microorganisms has been extensively investigated, there is only little experience with its application to animal tissue samples. Here, we show that a conventional one-dimensional LC-SRM workflow applied to mouse liver tissue suffers from a shortcoming in terms of sensitivity for lower abundance proteins. This problem could be solved through the extension of the standard workflow by an additional dimension of separation at the peptide level prior to online LC-SRM. For this purpose, we used off-gel electrophoresis (OGE) which is also shown to outperform strong cation exchange (SCX) in terms of resolution, gain of signal intensity, and predictability of separation. The extension of the SRM workflow by a high resolving peptide separation technique is an ideal combination as it allows the addition of stable isotope standards directly after trytic digestion and will increase the dynamic range of protein abundances amenable by SRM in animal tissue.

The tandem mass spectrometry techniques electron-induced dissociation (EID) and collision-activated dissociation (CAD) have been compared as tools for providing detailed structural information of polyketides. Polyketides are an important class of natural products that account for a significant proportion of the drugs currently in clinical use. Three polyketide natural products, namely erythromycin A, lasalocid A, and iso-lasalocid A, were subjected to both CAD and EID, and their fragment ions were assigned with sub-part-per-million accuracy. The number of fragment ions detected through EID was much greater than for CAD, leading to a greater amount of structural information obtained for each polyketide, albeit with a decreased signal-to-noise ratio. The effect of different bound cations on the fragment pattern of the isomers lasalocid A and iso-lasalocid A was studied, with CAD and EID performed on the [M + H]+, [M + Na]+, [M + Li]+, and [M + NH4]+ precursor ions. The lithiated species were found to produce the greatest degree of fragmentation and enabled detailed structural information on the isomers to be obtained. Multistage mass spectrometry (MS3) experiments, combining CAD and EID, could also be performed on the lithiated species, generating new fragment information which enables the two isomers to be distinguished. Combining CAD and EID for the structural characterization of polyketides will therefore be a useful tool for identifying and characterizing unknown polyketides and their biosynthetic intermediates.

The ultraweak chemiluminescence (CL) from the reaction of hydrogen peroxide and carbonate is strongly enhanced by the branched NaYF4:Yb3+/Er3+ nanoparticle (NP) in the presence of aqueous ammonia. It was explained that ammonia catalyzes the decomposition of peroxymonocarbonate, which is the product of hydrogen peroxide mixing with bicarbonate, making the formation of (CO2)2*, (O2)2*, and 1O2. The excitation energy, carried by these emitter intermediates, can be transferred to NaYF4:Yb3+/Er3+ NP. The CL intensity is directly proportional to the concentration of ammonia present in the solution. A flow-injection CL system with high sensitivity, selectivity, and reproducibility is proposed for the determination of aqueous ammonia. The proposed method exhibited advantages in a larger linear range from 0.5 μmol L–1 to 50 μmol L–1 and a lower detection limit of 1.1 × 10–8 mol L–1 (S/N = 3). This method has been successfully applied to the evaluation of ammonia in water samples with recoveries from 95% to 108%. The relative standard deviations are 1.8% and 4.1% for intra-assay and inter-assay precision, respectively.

Graphene oxide (GO) nanosheets were immobilized onto the capillary wall using 3-aminopropyldiethoxymethyl silane as coupling agent. Graphene coated column (G@column) was fabricated by hydrazine reduction of GO modified column. Scanning electron microscopy (SEM) images provided visible evidence of the GO grafted on the capillary wall. Energy dispersive X-ray spectrometry (EDS) indicated the high coverage of the GO on the capillary wall. The G@column exhibited a pH-dependent electroosmotic flow (EOF) from anode to cathode in the pH range of 3–9 while the graphene oxide coated column (GO@column) showed a constant EOF. Both GO@column and G@column were evaluated for open-tubular capillary electrochromatography (OT-CEC). The GO@column was also evaluated for open-tubular capillary liquid chromatography (OT-CLC). Good separation of the tested neutral analytes on the GO@column was achieved on the basis of a typical reversed-phase behavior. On the contrary, G@column showed poor separation performance because of the strong π–π stacking and hydrophobic interactions between graphene and polyaromatic hydrocarbons. The high coverage of GO improved the column phase ratio which makes the GO@column promising for OT-CLC separation. Five of the major known proteins including three glycoisoforms of ovalbumin in chicken egg white were identified in a single run on the GO@column with phosphate buffer (5 mM, pH 7.0) and an applied voltage of 20 kV. The run-to-run, day-to-day, and column-to-column reproducibilities are evaluated by calculating the relative standard deviations (RSDs) of the EOF in OT-CEC and retention time of naphthalene in OT-CLC, respectively. These RSD values were found to be less than 3%.

The determination of water in various matrices is one of the most important analytical measurements. We report on a high-resolution capacitance-based moisture sensor utilizing a thin film of a perfluorosulfonate ionomer (PFSI)–H3PO4 composite in a flow-through configuration, for both gas and liquid samples. Incorporation of H3PO4 into a PFSI sensing film improved the limit of detection (LOD) (signal-to-noise ratio, S/N = 3) by a factor of 16 in the gas phase to 0.075% relative humidity (RH) (dew point = −56 °C). The response time was dependent on the sensing film thickness and composition and was as low as ∼60 ms. The temperature dependence of the sensor response, and its relative selectivity over alcohol and various other solvents, are reported. Measurement of water in organic solvents was carried out in two different ways. In one procedure, the sample was vaporized and swept into the detector (e.g., in a gas chromatograph (GC) without a column); it permitted a throughput of 80 samples/h. This is well-suited for higher (%) levels of water. In the other method, a flow injection analysis system integrated to a tubular dialysis membrane pervaporizer (PV-FIA) was used; the LOD for water in ethanol was 0.019% (w/w). We demonstrated the temporal course of drying of ethanol by Drierite; the PV-FIA results showed excellent correspondence (r2 > 0.99) with results from GC–thermal conductivity detection. The system can measure trace water in many types of organic solvents; no reagent consumption is involved.