Exploring the expression bar code of SAA variants for gastric cancer detection.

We reported an integrated platform to explore serum protein variant pattern in cancer and its utility as a new class of biomarker panel for diagnosis. On the model study of serum amyloid A (SAA), we employed nanoprobe-based affinity mass spectrometry for enrichment, identification and quantitation of SAA variants from serum of 105 gastric cancer patients in comparison with 54 gastritis patients, 54 controls, and 120 patients from other cancer. The result revealed surprisingly heterogeneous and most comprehensive SAA bar code to date, which comprises 24 SAA variants including SAA1- and SAA2-encoded products, polymorphic isoforms, N-terminal-truncated forms, and three novel SAA oxidized isotypes, in which the variant-specific peptide sequence were also confirmed by LC-MS/MS. A diagnostic model was developed for dimension reduction and computational classification of the 24 SAA-variant bar code, providing good discrimination (AUC = 0.85 ± 3.2E-3) for differentiating gastric cancer group from gastritis and normal groups (sensitivity, 0.76; specificity, 0.81) and was validated with external validation cohort (sensitivity, 0.71; specificity, 0.74). Our platform not only shed light on the occurrence and modification extent of under-represented serum protein variants in cancer, but also suggested a new concept of diagnostic platform by serum protein variant profile.

BAD-lectins: boronic acid-decorated lectins with enhanced binding affinity for the selective enrichment of glycoproteins.

The weak and variable binding affinities exhibited by lectin-carbohydrate interactions have often compromised the practical utility of lectin in capturing glycoproteins for glycoproteomic applications. We report here the development and applications of a new type of hybrid biomaterial, namely a boronic acid-decorated lectin (BAD-lectin), for efficient bifunctional glycoprotein labeling and enrichment. Our binding studies showed an enhanced affinity by BAD-lectin, likely to be mediated via the formation of boronate ester linkages between the lectin and glycan subsequent to the initial recognition process and thus preserving its glycan-specificity. Moreover, when attached to magnetic nanoparticles (BAD-lectin@MNPs), 2 to 60-fold improvement on detection sensitivity and enrichment efficiency for specific glycoproteins was observed over the independent use of either lectin or BA. Tested at the level of whole cell lysates for glycoproteomic applications, three different types of BAD-lectin@MNPs exhibited excellent specificities with only 6% overlapping among the 295 N-linked glycopeptides identified. As many as 236 N-linked glycopeptides (80%) were uniquely identified by one of the BAD-lectin@MNPs. These results indicated that the enhanced glycan-selective recognition and binding affinity of BAD-lectin@MNPs will facilitate a complementary identification of the under-explored glycoproteome.

Coupling of single quantum emitters to plasmons propagating on mechanically etched wires.

We demonstrate the coupling of a single nitrogen vacancy center in a nanodiamond to propagating plasmonic modes of mechanically etched silver nanowires. The mechanical etch is performed on single crystalline silver nanoplates by the tip of an atomic force microscope cantilever to produce wires with pre-designed lengths. We show that single plasmon propagation can be obtained in these wires, thus making these structures a platform for quantum information processing.

A chemically functionalized magnetic nanoplatform for rapid and specific biomolecular recognition and separation.

We have developed a target-molecule-functionalized magnetic nanoparticle (MNP)-based method to facilitate the study of biomolecular recognition and separation. The superparamagnetic property of MNPs allows the corresponding biomolecules to be rapidly separated from crude biofluids with a significant improvement in recovery yield and specificity. Various MNPs functionalized with tag molecules (chitin, heparin, and amylose) were synthesized for recombinant protein purification, and several probe-functionalized MNPs, such as nitrilotriacetic acid (NTA)@MNP and P(k)@MNP, exhibited excellent extraction efficiency for proteins. In a cell recognition study, mannose-functionalized MNPs allowed specific purification of Escherichia coli with FimH adhesin on the surface. In an immunoprecipitation assay, the antibody-conjugated MNPs reduced the incubation time from 12 to 1 h while maintaining a comparable efficiency. The functionalized MNPs were also used in a membrane proteomic study that utilized the interaction between streptavidin-functionalized MNPs and biotinylated cell membrane proteins. Overall, the functionalized MNPs were demonstrated to be promising probes for the specific separation of targets from proteins to cells and proteomics.

Propagation of plasmons in designed single crystalline silver nanostructures.

We demonstrate propagation of plasmons in single crystalline silver nanostructures fabricated using a combination of a bottom-up and a top-down approach. Silver nanoplates of thickness around 65 nm and a surface area of about 100 µm(2) are made using a wet chemical method. Silver nanotips and nanowires are then sculptured by focused ion beam milling. The plasmons are excited by using the fluorescence from the redeposited silver clusters during the milling process. Propagation of plasmons in the nanowires is observed in the visible spectral region. We also observe a cavity effect by measuring the emission spectrum from the distal wire end.

Iron oxide nanomatrix facilitating metal ionization in matrix-assisted laser desorption/ionization mass spectrometry.

The significance and epidemiological effects of metals to life necessitate the development of direct, efficient, and rapid method of analysis. Taking advantage of its simple, fast, and high-throughput features, we present a novel approach to metal ion detection by matrix-functionalized magnetic nanoparticle (matrix@MNP)-assisted MALDI-MS. Utilizing 21 biologically and environmentally relevant metal ion solutions, the performance of core and matrix@MNP against conventional matrixes in MALDI-MS and laser desorption ionization (LDI) MS were systemically tested to evaluate the versatility of matrix@MNP as ionization element. The matrix@MNPs provided 20- to >100-fold enhancement on detection sensitivity of metal ions and unambiguous identification through characteristic isotope patterns and accurate mass (<5 ppm), which may be attributed to its multifunctional role as metal chelator, preconcentrator, absorber, and reservoir of energy. Together with the comparison on the ionization behaviors of various metals having different ionization potentials (IP), we formulated a metal ionization mechanism model, alluding to the role of exciton pooling in matrix@MNP-assisted MALDI-MS. Moreover, the detection of Cu in spiked tap water demonstrated the practicability of this new approach as an efficient and direct alternative tool for fast, sensitive, and accurate determination of trace metal ions in real samples.

Terminal Groups-Dependent Near-Field Enhancement Effect of Ti3C2Tx Nanosheets.

Both multilayered (ML) and few-layered (FL) Ti3C2Tx nanosheets have been prepared through a typical etching and delaminating procedure. Various characterizations confirm that the dominant terminal groups on ML-Ti3C2Tx and FL-Ti3C2Tx are different, which have been assigned to O-related and hydroxyl groups, respectively. Such deviation of the dominant terminals results in the different physical and chemical performance and eventually makes the nanosheets have different potential applications. In particular, before coupling to Ag nanoparticles, ML-Ti3C2Tx can present stronger near-field enhancement effect; however, Ag/FL-Ti3C2Tx hybrid structure can confine stronger near-field due to the electron injection, which can be offered by the terminated hydroxyl groups.

Caffeic acid phenethyl ester and its related compounds limit the functional alterations of the isolated mouse brain and liver mitochondria submitted to in vitro anoxia-reoxygenation: relationship to their antioxidant activities.

It is an important therapeutic strategy to protect mitochondria from oxidative stress, especially during ischemia-reperfusion. In the present study, an attempt has been made to evaluate the protective effects of caffeic acid phenethyl ester (CAPE) and its related phenolic compounds on mouse brain and liver mitochondria injury induced by in vitro anoxia-reoxygenation. Added before anoxia or reoxygenation, CAPE markedly protected coupled respiration with the decrease in state 4 and the increases in state 3, respiratory control ratio (RCR) and ADP/O ratio in a concentration-dependent manner. CAPE effectively protected mitochondria by inhibiting the mitochondrial membranes fluidity decrease, the lipoperoxidation and the protein carbonylation increase, which indicated its protective action against the mitochondrial oxidative damage. Meanwhile, CAPE blocked the enhanced release of cardiolipin (CL) and cytochrome c (Cyt c). The related phenolic compounds like caffeic acid (CA), ferulic acid (FA) and ethyl ferulate (EF) also had different-degree protective effects. CAPE and CA were more potent than FA and EF. Their structural differences played the key role in their activity levels. These results suggest that CAPE and its related phenolic compounds protect mitochondria mainly correlated to their antioxidative activities and may be of interest for the prevention and therapy of ischemia-reperfusion injuries.

Electrophoretic method for the identification of a haze-active protein in grape seeds.

A simple, fast, and more selective approach is presented in this study for the identification of haze-active proteins. Grape seed proteins were unfolded by 1% SDS and then interacted with different amounts of tannin at 4 degrees C, followed by gel electrophoresis. It was found that the intensity of the band at 45 kDa was decreased as tannins increased. The amino acid composition of this isolated 45-kDa protein was higher in proline (9.49%) than the average proline content of total grape seed proteins (4.85%). To verify the selectivity of the proposed method, a globular protein (bovine serum albumin, BSA) and a proline-rich protein (gelatin) were selected and used in the model system. As expected, gelatin was removed as it reacted with the increasing added tannins, whereas BSA did not. These results showed that it is possible to identify haze-active proteins by modulating the accessibility of protein to tannins, suggesting this new method can be used by the beverage industry to trouble-shoot haze problems and for quality control.

Nanoparticle-assisted MALDI-TOF MS combined with seed-layer surface preparation for quantification of small molecules.

Despite the advantages of simplicity and high-throughput detection that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has over other methods, quantitative analysis of low-molecular-weight analyte is hampered by interference from matrix-derived background noise and signal fluctuation due to the inhomogeneous MALDI sample surface. Taking advantage of improved sample homogeneity through matrix-conjugated magnetic nanoparticles (matrix@MNP) and the seed-layer method, we report a new strategy for the rapid identification and quantification of drugs in urine samples, using morphine and 7-aminoflunitrazepam (7-aminoFM2) as model compounds. To our knowledge, this is the first attempt using the seed-layer method for small molecule analysis. By applying the proposed seed-layer method, which was specifically optimized for the 2,5-dihydroxybenzoic acid@MNP (DHB@MNP) matrix, homogeneous sample crystallization examined by microscopy analysis was obtained that generated reproducible MALDI signals (RSD<10.0%). For urine sample analysis, simple liquid-liquid extraction as a sample pretreatment step effectively reduced the ion suppression effect caused by the endogenous components in urine; good recoveries (82-90%) were obtained with a small ion suppression effect (<14% of signal decrease). This newly developed method demonstrated good quantitation linearity over a range of 50-2000 ng mL(-1) (R(2)>0.996) with reduced signal variation (RSD<10.0%). The detection limit is 30 ng mL(-1) with good precision (intra-day, 2.0-9.3%; inter-day, 5.0-10.0%) and accuracy (intra-day, 95.0-106.0%; inter-day, 103.0-115.5%). The nanoparticle-assisted MALDI-TOF MS combined with seed-layer surface preparation provides a rapid, efficient and accurate platform for the quantification of small molecules in urine samples.

Dihydrobenzoic acid modified nanoparticle as a MALDI-TOF MS matrix for soft ionization and structure determination of small molecules with diverse structures.

Efficient structural characterization is important for quality control when developing novel materials. In this study, we demonstrated the soft ionization capability of the hybrid of immobilized silica and 2,5-dihydrobenzoic acid (DHB) on iron oxide magnetic nanoparticles in MALDI-TOF MS with a clean background. The ratio between SiO(2) and DHB was examined and was found to affect the surface immobilization of DHB on the nanoparticle, critically controlling the ionization efficiency and interference background. Compared with commercial DHB, the functionalized nanoparticle-assisted MALDI-TOF MS provided superior soft ionization with production of strong molecular ions within 5 ppm mass accuracy on a variety of new types of synthetic materials used for solar cells, light emitting devices, dendrimers, and glycolipids, including analytes with either thermally labile structures or poor protonation tendencies. In addition, the enhancements of the molecular ion signal also provided high-quality product-ion spectra allowing structural characterization and unambiguous small molecule identification. Using this technique, the structural differences among the isomers were distinguished through their characteristic fragment ions and comprehensive fragmentation patterns. With the advantages of long-term stability and simple sample preparation by deposition on a regular sample plate, the use of DHB-functionalized nanoparticles combined with high-resolution MALDI-TOF MS provides a generic platform for rapid and unambiguous structure determination of small molecules.