Enrichment and desalting of tryptic protein digests and the protein depletion using boron nitride

Sample preparation still remains a great challenge in modern bioanalysis and the interest in new efficient solid phase extraction (SPE) materials still remains high. In this work, hexagonal boron nitride (h-BN) is introduced as a new SPE material for the isolation and enrichment of peptides. The h-BN is isoelectronic and structurally similar to graphite. It has remarkable properties including good thermal conductivity, excellent thermal and chemical stability and a better oxidation resistance than graphite. BN attracts increasing interest because of its wide range of applicability. In the present work, the great potential of h-BN, as a new SPE-material, on the enrichment, preconcentration and desalting of tryptic digest of model proteins is demonstrated. A special attention was dedicated to the efficient enrichment of hydrophilic phosphopeptides. Two elution protocols were developed for the enrichment of peptides compatible for subsequent MALDI-MS and ESI-MS analysis. In addition, the recoveries of 5 peptides and 3 phosphopeptides with wide range of pI values utilizing h-BN materials with different surface areas were investigated. 84–106% recovery rate could be achieved using h-BN materials. The results were compared with those obtained using graphite and silica C18 under the same elution conditions, and lower recoveries were obtained. In addition, h-BN was found to have a capability of protein depletion, which is requisite for the peptide profiling.     

抚顺地区大气总悬浮微粒元素浓度季节变化的研究

本文采用X射线荧光法对抚顺地区大气总悬浮微粒（TSP）中S等20种元素的浓度水平进行分析，并通过无素的富集因子分析探讨TSP元素富集特征和污染来源，结果表明：采用暖期TSP浓度水平明显超过国家三级标准，其中富集程度较高的S，As,Zn等主要来源于煤炭燃烧。     

Study on the etching conditions of polycarbonate detectors for particle analysis of safeguards environmental samples

The fission track technique was applied to the particle analysis for safeguards environmental samples to obtain information about the isotope ratio of nuclear materials in individual particles. To detect the particles containing nuclear material with high detection efficiency and less particle loss, the influence of uranium enrichments on etching conditions of a fission track detector made of polycarbonate was investigated. It was shown that the increase in uranium enrichment shortened the suitable etching time both for particle detection and for less particle loss. From the results obtained, it was suggested that the screening of the uranium particles according to the enrichment is possible by controlling the etching time of the detector.     

用硅烷化处理改性硅胶分离富集痕量元素

将硅胶用二氯二甲基硅烷处理后，能降低硅胶对极性物质的吸附，增加其对非极性物质或弱极性物质如５－Ｂｒ－ＰＡＤＡＰ等大多数螯合剂的吸附，同时使改性硅胶适应的ＰＨ范围扩宽，对金属离子的净化学吸附增大，使用寿命增加。     

Inductively coupled plasma optical emission spectrometric determination of trace element in PM10 airborne particulate matter collected in an industrial area of Argentina

Trace metals of relevance from the environmental and toxicological point of view were quantified in the city of Campana, Buenos Aires, Argentina. The collection of particulate matter was performed on ash-free fiber glass filters using high-volume samplers with a PM₁₀ sampling head, during a 3-month period in 2002. An acid leaching of elements deposited on the filters was adopted paying special attention to the recovery of volatile elements. Analysis was performed by inductively coupled plasma optical emission spectrometry (ICP OES) to ascertain the concentrations of 12 key elements, namely, Al, As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, Ti, V and Zn. The validation of the procedure was performed by the analysis of the standard reference material NIST 1648, urban particulate matter, and good agreement between concentrations found and the reported certified values was achieved. Blank filters were spiked with the analytes investigated and the recoveries varied between 83% and 92%. Metal concentrations spanned the range 0.03 ng m⁻³ (equivalent to 0.42 μg g⁻¹) for Cd to 1.9 μg m⁻³ (equivalent to 29.7 mg g⁻¹) for Fe. The results obtained show that the pollutants of special environmental and health concern are As and Pb. Mean As concentration was higher than the guideline value associated with an excess cancer risk of 1:10⁻⁶, reported by the World Health Organization (WHO). Lead is the only element that showed higher concentrations than those recently measured in the large and heavily trafficked metropolitan area of Buenos Aires. Cadmium>Pb>As>Zn>Cu are the elements more enriched in airborne PM₁₀.     

Community benchmarks for virtual screening

Ligand enrichment among top-ranking hits is a key metric of virtual screening. To avoid bias, decoys should resemble ligands physically, so that enrichment is not attributable to simple differences of gross features. We therefore created a directory of useful decoys (DUD) by selecting decoys that resembled annotated ligands physically but not topologically to benchmark docking performance. DUD has 2950 annotated ligands and 95,316 property-matched decoys for 40 targets. It is by far the largest and most comprehensive public data set for benchmarking virtual screening programs that I am aware of. This paper outlines several ways that DUD can be improved to provide better telemetry to investigators seeking to understand both the strengths and the weaknesses of current docking methods. I also highlight several pitfalls for the unwary: a risk of over-optimization, questions about chemical space, and the proper scope for using DUD. Careful attention to both the composition of benchmarks and how they are used is essential to avoid being misled by overfitting and bias.     

Bias, reporting, and sharing: computational evaluations of docking methods

Computational methods for docking ligands to protein binding sites have become ubiquitous in drug discovery. Despite the age of the field, no standards have been established with respect to methodological evaluation of docking accuracy, virtual screening utility, or scoring accuracy. There are critical issues relating to data sharing, data set design and preparation, and statistical reporting that have an impact on the degree to which a report will translate into real-world performance. These issues also have an impact on whether there is a transparent relationship between methodological changes and reported performance improvements. This paper presents detailed examples of pitfalls in each area and makes recommendations as to best practices.     

Applications of aptamers in cancer cell biology

Identifying cells associated with specific disease states is critically important for the early detection and diagnosis of cancer. To facilitate this task, molecular probes, which bind biomarkers that are either specifically or differentially expressed in diseased cells relative to healthy cells, provide a simple and effective method. This review focuses on the use of DNA aptamers as molecular probes for cancer cells. These aptamers are created by means of the cell-based Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, which uses whole disease cells as targets. We describe at length the steps of the cell-SELEX process and discuss several applications for the aptamers, including profiling leukemia patient samples and discovering cell-surface cancer biomarkers. We conclude with a discussion of an aptamer-conjugated nanoparticle enrichment and detection scheme.     

The preparation of high-capacity boronate affinity adsorbents by surface initiated reversible addition fragmentation chain transfer polymerization for the enrichment of ribonucleosides in serum

Boronate affinity adsorption is uniquely selective for cis-diol-containing molecules. The preparation and application of boronate affinity materials has attracted much attention in recent years. In this work, a high-capacity boronate affinity adsorbent was prepared by surface-initiated reversible addition–fragmentation chain transfer polymerization (SI-RAFT). Commercial aminated poly(glycidyl methacrylate) (PGMA) microspheres were modified with the chain transfer agent (CTA) S-1-dodecyl-S-(α,α-dimethyl-α-acetic acid)trithiocarbonate (DDATC). Boronate-affinity adsorbents were then prepared via SI-RAFT polymerization employing 3-acrylamidophenylboronic acid (AAPBA) as the monomer. The Fourier transform infrared spectroscopy (FT-IR), nitrogen adsorption and desorption measurements have proven the successful grafting of AAPBA on PGMA microspheres surface. The boronate affinity adsorbents thus prepared possess much higher adsorption capacity (99.2 µmol/g of adenosine) and both faster adsorption and desorption speed towards ribonucleosides, the adsorption and desorption could be completed in 2 min. The high selectivity of the adsorbents to ribonucleosides was verified in the presence of a large excess of deoxynucleosides. The boronate affinity adsorbents were then employed for sample pretreatment before HPLC analysis of ribonucleosides in serum. The ribonucleosides were effectively enriched by boronate affinity dispersive solid-phase extraction (BA-DSPE), with high mass recoveries and good precision. The simultaneous determination of uridine and guanosine in calf serum was achieved by utilizing the standard addition method, their contents were determined to be 170 ± 11.6 ng/mL and 39.6 ± 4.4 ng/mL respectively. The results proved that the prepared boronate affinity materials could be applied for sample pretreatment of cis-diol containing molecules in biological samples.     

4-Mercaptophenylboronic acid functionalized graphene oxide composites: Preparation,characterization and selective enrichment of glycopeptides

Selective enrichment and isolation of glycopeptides from complex biological samples was indispensable for mass spectrometry (MS)-based glycoproteomics, however, it remained a great challenge due to the low abundance of glycoproteins and the ion suppression of non-glycopeptides. In this work, 4-mercaptophenylboronic acid functionalized graphene oxide composites were synthesized via loading gold nanoparticles on polyethylenimine modified graphene oxide surface, followed by 4-mercaptophenylboronic acid immobilization by the formation of Au–S bonding (denoted as GO/PEI/Au/4-MPB composites). The composites showed highly specific and efficient capture of glycopeptides due to their excellent hydrophilicity and abundant boronic acid groups. The composites could selectively capture the glycopeptides from the mixture of glycopeptides and nonglycopeptides, even when the amounts of non-glycopeptides were 100 times more than glycopeptides. Compared with commercial meta-amino phenylboronic acid agarose, the composites showed better selectivity when the sample was decreased to 10 ng. These results clearly verified that the GO/PEI/Au/4-MPB composites might be a promising material for glycoproteomics analysis.