Mass Spectrometry-based Deep Coverage Proteome:Evaluation of Cellular Protein Extraction Methods

The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.

Enzymatic Determination of Glucose by Optical-Fiber Sensor Sequential Injection Renewable Surface Spectrophotometry

On the basis of oxidative decoloration of bromopyrogallol red （BPR） with H2O2, catalyzed by horseradish peroxidase（ HRP）, and the sequential injection renewable surface technique（ SI-RST）, a highly sensitive optical-fiber sensor spectrophotometric method for the enzymatic determination of hydrogen peroxide was proposed. By coupling with a glucose oxidase（GOD）-catalyzed reaction, the method was used to determine glucose in human serum. The considerations in system and flow cell design, and factors that influence the determination performance are discussed. With 100μL of sample loaded and 0. 6 mg of bead trapped, the linear response range from 5.0 × 10^-8 to 5.2 × 10^-6 mol/L BPR with a detection limit（3σ） of 2. 5 ×10 ^-8 mol/L BPR, and a precision of 1.1% RSD（ n = 11 ） and a throughput of a 80 samples per hour can be achieved. Under the conditions of a 8. 7 × 10^ -6 mol/L BPR substrate, 0. 04 unit/mL HRP, 600 s reaction time and a reaction temperature of 37℃, the linear response range for H2O2 was from 5.0 × 10^-8 to 7.0 × 10^-6 mol/L with a detection limit（3σ） of 1.0 × 10^-8 mol/L and a precision of 3.7% RSD （ n = 11 ）. The linear response range by coupling with a GOD-catalyzed reaction was from 1.0 × 10^-7 to 1.0 × 10^-5 mol/L. The method was directly applied to determine glucose in human serum. Glucose contents obtained by the proposed procedure were compared with those obtained by using the phenol-4-AAP method, the error was found to be less than 3%.

A shape-reconfigurable,light and magnetic dual-responsive shape-memory micropillar array chip for droplet manipulation

Droplet manipulation on an open surface has great potential in chemical analysis and biomedicine engineering.However,most of the reported platforms designed for the manipulation of water droplets cannot thoroughly solve the problem of droplet evaporation.Herein,we report a shape-reconfigurable micropillar array chip for the manipulation of water droplets,oil droplets and water-in-oil droplets.Water-in-oil droplets provide an enclosed space for water droplets,preventing the evaporation in an open environment.Perfluoropolyether coated on the surface of the chip effectively reduces the droplet movement resistance.The micropillar array chip has light and magnetic dual-response due to the Fe3O4 nanoparticles and the reduced iron powder mixed in the shape-memory polymer.The micropillars irradiated by a near-infrared laser bend under the magnetic force,while the unirradiated micropillars still keep their original shape.In the absence of a magnetic field,when the micropillars in a temporary shape are irradiated by the near-infrared laser to the transition temperature,the micropillars return to their initial shape.In this process,the surface morphology gradient caused by the deformation of the micropillars and the surface tension gradient caused by the temperature change jointly produce the driving force of droplet movement.

Revealing the Regulation Effect of Surface Charge at Aromatic Interface to Dynamic Conformational Changes of α-Synuclein at Early Aggregation Stage

The aggregation ofα-synuclein(α-syn)is strongly influenced by membrane interfaces,but the mechanism of transition from monomers to oligomers at early aggregation stage is not clear.Here,we investigate the adsorption and structure changes ofα-syn on oppositely charged aromatic interfaces through in-situ surface-enhanced infrared absorption(SEIRA)spectroscopy and nano-IR technique.The results show that the synergy of electrostatic and hydrophobic interactions leads to a“fast-slow”two-step aggregation pathway on negatively charged interface.Surface adsorption induces the formation of an extended helix structure and subsequently partial helix unwinding in NAC region,which enables the hydrophobic stacking between nearby NAC regions.Stable antiparallel β-sheet rich aggregates are gradually emerging as further interactions of monomers with the fast formed“first layer”.Monomers electrostatically adsorb on positively charged interface by C-terminus with NAC region and N-terminus stretched in solvent,which serve as an aggregation core and induce further adsorption and gradual formation of aggregates with C-terminus exposure.Our results demonstrate the modulation of surface charge and synergy of electrostatic and hydrophobic interactions on the interaction modes and aggregation pathways,which provide insights into dynamic conformation changes ofα-syn at early aggregation stage and imply the important role of spatial-temporal heterogeneity of membranes inα-synucleinopathies.

Rational Design of Capping Ligands of Quantum Dots for Biosensing

Quantum dots have been widely applied in biosensing due to their outstanding optical properties.The emissions of quantum dots are mainly determined by their composition and size,as described by the Brus’s equation.Somehow,in this case,their emissions are hardly regulated reversibly and responsively,which are unsuitable for biosensing and biodetection.In the last decade,capping ligands have been used for designing biosensors because of their responsive regulation on the photoluminescence of quantum dots.Here,we first summarize the advances in characterization and calculation specific for ligands,which have helped to provide insights into the photoluminescence process and energy band theory of quantum dots.We then review two ways of ligand design that influence the optical properties of quantum dots:affecting the process of photoluminescence,or the orbital/electronic structure.In the latter case,the atoms on both the ligand and the surface of the quantum dot interact to affect the energy band structure of the quantum dot core.Examples are presented of how these quantum dots that possess responsive properties due to the design of the ligands have been applied to sensing.With further exploration,we hope to see advances in the fundamental understanding of the energy band structures and practical applications of these quantum dots.

Nitrogen-doped fluorescence carbon dots as multi-mechanism detection for iodide and curcumin in biological and food samples

Iodine ion is one of the most indispensable anions in living organisms,particularly being an important substance for the synthesis of thyroid hormones.Curcumin is a yellow-orange polyphenol compound derived from the rhizome of Curcuma longa L.,which has been commonly used as a spice and natural coloring agent,food additives,cosmetics as well as Chinese medicine.However,excess curcumin may cause DNA inactivation,lead to a decrease in intracellular ATP levels,and trigger the tissue necrosis.Therefore,quantitative detection of iodine and curcumin is of great significance in the fields of food and life sciences.Herein,we develop nitrogen-doped fluorescent carbon dots(NCDs)as a multi-mechanism detection for iodide and curcumin in actual complex biological and food samples,which was prepared by a one-step solid-phase synthesis using tartaric acid and urea as precursors without adding any other reagents.An assembled NCDs-Hg^(2+) fluorescence-enhanced sensor for the quantitative detection of I^(-) was established based on a fluorescence“turn-off-on”mechanism in a linear range of 0.3-15μM with a detection limit of 69.4 nM and successfully quantified trace amounts of I^(-) in water samples and urine sample.Meanwhile,the as-synthesized NCDs also can be used as a fluorescent quenched sensor for curcumin detection based on the synergistic internal filtration effect(IFE)and static quenching,achieving a good linear range of 0.1-20μM with a satisfactory detection limit of 29.8 nM.These results indicate that carbon dots are potential sensing materials for iodine and curcumin detection for the good of our health.

Improvement of antibacterial activity of copper nanoclusters for selective inhibition on the growth of gram-positive bacteria

In general, copper nanoclusters (CuNCs) possess very low or even virtually no bactericidal effect. Herein,we report a novel CuNCs possessing significantly high antibacterial activity, that is tannic acid (TA)capped CuNCs (TA-CuNCs). TA-CuNCs exhibit strong absorption and excitation-dependent fluorescence within pH 2-12, resulting from the functional groups of TA-CuNCs due to two prototropic equilibria,phenolphenolate and carboxyliccarboxylate. There exists synergistic effect of TA and copper nanoclusters which endows TA-CuNCs remarkable antibacterial capability as a microbicide, as characterized by the effective inhibition on the growth of gram-positive bacteria by damaging the cell membrane. By incubating 1 x 10~7 CFU/mL of gram-positive bacteria Staphylococcus aureus and Bacillus subtilis with 30 μg/mL of TA-CuNCs for 10 min, the bacteria are completely inhibited, while under same conditions the viabilities of gram-negative bacteria Escherichia coli 0157:H7 and Pseudomonas aeruginosa remain 85.0%, 72.0%, respectively. In addition, TA-CuNCs exhibit low cytotoxicity and favorable biocompatibility demonstrated by standard methyl thiazolyl tetrazolium (MTT) assay with HepG2 and 293 Tcells, giving rise to cell viability of 94.2% for HepG2 and 96.7% for 293 T by incubating 10~6 cell/mL with 200 μg/mL of TA-CuNCs for 24 h. These results make TA-CuNCs a potential alternative as bactericide for infection treatment caused by gram-positive bacteria.

A variable importance criterion for variable selection in near-infrared spectral analysis

Variable selection is a universal problem in building multivariate calibration models, such as quantitative structure-activity relationship(QSAR) and quantitative relationships between quantity or property and spectral data. Significant improvement in the prediction ability of the models can be achieved by reducing the bias induced by the uninformative variables. A new criterion,named as C, is proposed in this study to evaluate the importance of the variables in a model. The value of C is defined as the average contribution of a variable to the model, which is calculated by the statistics of the models built with different combinations of the variables. In the calculation, a large number of partial least squares(PLS) models are built using a subset of variables selected by randomly re-sampling. Then, a vector of the prediction errors, in terms of root mean squared error of cross validation(RMSECV), and a matrix composed of 1 and 0 indicating the selected and unselected variables can be obtained. If multiple linear regression(MLR) is employed to model the relationship between the RMSECVs and the matrix, the coefficients of the MLR model can be used as a criterion to evaluate the contribution of a variable to the RMSECV. To enhance the efficiency of the method, a multi-step shrinkage strategy was used. Comparison with Monte Carlo-uninformative variables elimination(MC-UVE), randomization test(RT) and competitive adaptive reweighted sampling(CARS) was conducted using three NIR benchmark datasets. The results show that the proposed criterion is effective for selecting the informative variables from the spectra to improve the prediction ability of models.

A modular single-cell pipette microfluidic chip coupling to ETAAS and ICP-MS for single cell analysis

Accurate single-cell capture is a crucial step for single cell biological and chemical analysis. Conventional single-cell capturing often confront operational complexity, limited efficiency, cell damage, large scale but low accuracy, incompetence in the acquirement of nano-upgraded single-cell liquid. Flow cytometry has been widely used in large-scale single-cell detection, while precise single-cell isolation relies on both a precision operating platform and a microscope, which is not only extremely inefficient, but also not conducive to couple with modern analytical instruments. Herein, we develop a modular single-cell pipette(m SCP) microfluidic chip with high efficiency and strong applicability for accurate direct capture of single viable cell from cell suspensions into nanoliter droplets(30-1000 n L). The m SCP is used as a sampling platform for the detection of Cd Te quantum dots in single cells with electrothermal atomic absorption spectrometry(ETAAS) for the first time. It also ensures precise single-cell sampling and detection by inductively coupled plasma mass spectrometry(ICP-MS).

Dual functional AgNPs-M13 phage composite serves as antibacterial film and sensing probe for monitoring the corrosion of chromium-containing dental alloys

The preparation of silver nanoparticles(AgNPs)with microbe or plant tissues as bio-template offers green approach,while it suffers from low harvest and purification is needed.Herein,we propose a facile protocol for one-pot preparation of AgNPs using M13 phage as bio-template by simply mixing AgN03 solution with alkali M13 phage.In the obtained AgNPs-M13 phage composite,Cr(Ⅲ)selectively coordinates with the amino residues on phage surface and leads to the aggregation of AgNPs through the bridging of M13 phages.This makes it feasible for colorimetric sensing of Cr(Ⅲ)by measuring the absorbance ratio of AgNPs at 600 and 405 nm,which provides a LOD of 14 nmol/L.The composite also showed favorable bactericidal activity for both Gram-positive and Gram-negative bacteria,making it a promising candidate as antibacterial film in chromium-containing dental alloys and meanwhile serve as a sensing probe for monitoring the corrosion of the dental alloys.

Exploring fluorescent covalent organic frameworks for selective sensing of Fe^3＋

Covalent organic frameworks （COFs） have been widely applied in gas capture and separation, but the fluorescent property of COFs with large n-conjugated system tends to be underexplored. Here we report the fluorescent properties of several COFs including TaTa, DhaTab, TRITER- 1 and TzDa and the effect of metal ions of Na＋, Mg2＋, K＋, Ca2＋, Cu2＋, Zn2＋, Pb2＋, Ag＋, Cd2＋ and Fe3＋ on the fluorescence of these COFs. The results show that only Fe3＋ significantly quenched the fluorescence of the studied COFs. The possibility of the four COFs for selective sensing of Fe3＋ was demonstrated. The possible mechanism of the effect of Fe3＋ on the fluorescence of the COFs was based on the absorption competition quenching.

Rapid Determination of Amino Acids in Ginseng by High Performance Liquid Chromatography and Chemometric Resolution

Ginseng is one of the most important traditional Chinese medicines and functional foods.A method for the fast determination of amino acids in ginseng samples using high performance liquid chromatography（HPLC） was developed,in which strong isocratic elution was employed for simplifying the separation and speeding up the analysis.All amino acids were eluted within 3 min with the chromatogram composed of overlapped peaks from the interferences.Then,non-negative immune algorithm（NNIA） was adopted to resolve the chromatographic signals of the components from the chromatogram measured.The results show that the signals of the amino acids can be correctly extracted by NNIA and the signal extracted can be used for the quantitative analysis.The method was validated via determining six amino acids of four different samples of ginseng.The recoveries of the spiked samples are in a range of 96.6％-106.3％.

Mn-doped ZnS quantum dots/methyl violet nanohybrids for room temperature phosphorescence sensing of DNA

Mn-doped ZnS quantum dots/methyl violet nanohybrids were explored to develop a novel room temperature phosphorescence (RTP) sensor for the detection of DNA. Methyl violet (MV) as the electron acceptors was adsorbed on the surface of the quantum dots (QDs) to quench the RTP of the Mn-doped ZnS QDs through an electron-transfer process under excitation. The addition of DNA recovered the RTP signal of the Mn-doped ZnS QDs due to the binding of MV with DNA and the removal of MV from the surface of the Mn-doped ZnS QDs. Under the optimal conditions, the enhanced RTP intensity of the Mn-doped ZnS QDs/MV nanohybrids linearly increased with the concentration of DNA from 0.08 to 12 mg L-1 with the detection limit of 33.6 μg L-1. The relative standard deviation for eleven replicate detections of the reagent blank was 3.7%. The developed method was applied to the detection of DNA in spiked urine samples with recoveries of 96%-103% without interference from nonspecific fluorescence.

Recent advances in flow-based sample pretreatment for the determination of metal species by atomic spectrometry

During the last few years,various flow-based separation/preconcentration methodologies have gained pertinent novel advances and exhibited powerful capability in the field of sample pretreatment and their hyphenation with detection by atomic spectrometry.The present mini-review presents and discusses the progress of flow-based sample processing approaches commonly used for the assay of trace elemental species with detection by atomic spectrometry,including preliminary sample pretreatment,solid phase extraction(including solid phase microextraction),liquid-liquid extraction,vapor generation and dialysis techniques.Special emphasis has been paid on the novel applications and analytical procedures hyphenated with atomic spectrometry.The future perspectives of flow-based sample pretreatment protocols in the determination of trace elements and their speciation are also discussed.

A practical approach for near infrared spectral quantitative analysis of complex samples using partial least squares modeling

The number of latent variables (LVs) or the factor number is a key parameter in PLS modeling to obtain a correct prediction. Although lots of work have been done on this issue, it is still a difficult task to determine a suitable LV number in practical uses. A method named independent factor diagnostics (IFD) is proposed for investigation of the contribution of each LV to the predicted results on the basis of discussion about the determination of LV number in PLS modeling for near infrared (NIR) spectra of complex samples. The NIR spectra of three data sets of complex samples, including a public data set and two tobacco lamina ones, are investigated. It is shown that several high order LVs constitute main contributions to the predicted results, albeit the contribution of the low order LVs should not be neglected in the PLS models. Therefore, in practical uses of PLS for analysis of complex samples, it may be better to use a slightly large LV number for NIR spectral analysis of complex samples.

Near-infrared diffuse reflectance spectroscopy with sample spots and chemometrics for fast determination of bovine serum albumin in micro-volume samples

Near-infrared diffuse reflectance spectroscopy （NIRDRS） has attracted more and more attention in analyzing the components in samples with complex matrices. However, to apply this technique to micro-analysis, there are still some obstacles to overcome such as the low sensitivity and spectral overlapping associated with this approach. A method for fast determination of bovine serum albumin （BSA） in micro-volume samples was studied using NIRDRS with sample spots and chemometric techniques. 10 p^L of sample spotted on a filter paper substrate was used for the spectral measurements. Quantitative analysis was obtained by partial least squares （PLS） regression with signal processing and variable selection. The results show that the correlation coefficient （R） between the predicted and the reference concentration is 0.9897 and the recoveries are in the range of 87.4%-114.4% for the validation samples in the concentration range of 0.61-8.10 mg/mL. These results suggest that the method has the potential to quickly measure proteins in micro-volume solutions.

A variable differential consensus method for improving the quantitative near-infrared spectroscopic analysis

Consensus methods have presented promising tools for improving the reliability of quantitative models in near-infrared(NIR) spectroscopic analysis.A strategy for improving the performance of consensus methods in multivariate calibration of NIR spectra is proposed.In the approach,a subset of non-collinear variables is generated using successive projections algorithm(SPA) for each variable in the reduced spectra by uninformative variables elimination(UVE).Then sub-models are built using the variable subsets and the calibration subsets determined by Monte Carlo(MC) re-sampling,and the sub-model that produces minimal error in cross validation is selected as a member model.With repetition of the MC re-sampling,a series of member models are built and a consensus model is achieved by averaging all the member models.Since member models are built with the best variable subset and the randomly selected calibration subset,both the quality and the diversity of the member models are insured for the consensus model.Two NIR spectral datasets of tobacco lamina are used to investigate the proposed method.The superiority of the method in both accuracy and reliability is demonstrated.

Chemometric methods for extracting information from temperature-dependent near-infrared spectra

Temperature-dependent near-infrared(NIR) spectroscopy is a new technique for measuring the NIR spectra of a sample at different temperatures. Taking the advantage of the temperature effect, the technique has shown its potential in both quantitative and qualitative analysis. The technique has been proved to be powerful in determination of the analytes in complex samples,particularly in studying the functions of water in aqueous systems due to the significant effect of temperature on the NIR spectra of water. Because of the complicated interactions in the samples and the overlapping of the broad peaks in NIR spectra, it is difficult to extract the temperature-dependent information from the spectra. Chemometric methods, therefore, have been developed for improving the spectral resolution and extracting the temperature-induced spectral information. In this review, recent advances in the studies of chemometric methods and the applications in resolution, quantitative and structural analysis of temperature-dependent NIR spectra were summarized.

Structural engineering design of carbon dots for lubrication

Carbon dots(CDs)have opened up a new field of carbon nanomaterials and successively attracted increasing attention since their discovery in 2004.Owing to their ultrasmall size,tunable surface functional groups,excellent dispersibility,attractive stability,low toxicity,environmental friendliness,facile synthesis and low-cost precursors,CDs have been developed as green and promising frictionreducing and anti-wear materials in lubrication science,applied to energy conservation and extension of mechanical service life in recent years.However,there are few reviews focusing on the application of CDs in the important field of lubrication.In this review,we comprehensively summarize the development of CDs in lubrication for the first time.Firstly,three strategies for structural engineering design of CDs to improve their tribological characteristics are fully analyzed,in terms of size and shape control,surface modification and heteroatom doping.Secondly,the advance in lubrication application of CDs,including CDs as additives for lubricants,greases,gel and magnetorheological fluids as well as CDs as lubricating coatings,is systematically highlighted.Thirdly,the lubricating mechanisms of CDs as additives are introduced in detail.Furthermore,the remaining major challenges and opportunities for CDs in lubrication field are discussed and outlined.

Recent advances in the targeted fluorescent probes for the detection of metastatic bone cancer

Tumors of the breast,prostate,and lung are most likely to metastasize to the bone and typically indicates a poor cure and survival rate in cancer patients.Detection of metastatic bone cancer in early stage would save many lives and greatly improve patients’quality of life.Clinically,bone scintigraphy is often utilized to visualize bone metastases due to its relatively low cost and high sensitivity.Recently,a growth number of analytical researches aimed at developing targeted fluorescent probes to noninvasively image bone metastases with improved spatial resolution and specificity has been reported.In this review,we will summarize and discuss the recent published fluorescent probes on the accurate detection of metastatic bone cancer.First,the design principles of various targeted probes for imaging bone metastases will be presented,highlighting the signal moieties,targeting ligands,and physicochemical properties of the bone-specific probes.Next,the up-to-date bone-targeting fluorescent probes will be summarized and overviewed.Finally,future perspectives and challenges confronting the researchers in this field will be discussed.We believe this review will encourage novel ideas to develop smart targeted molecular probes for bone metastasis imaging,image-guided surgery,and therapeutic imaging materials.