MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry based targeted quantitative proteomics platform

Mass spectrometry (MS)‐based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS‐based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. In such approaches, synthetic reference peptides that are the stable isotope labeled version of proteotypic peptides of proteins to be quantitated are used as internal standards enabling specific identification and absolute quantification of targeted peptides. The quantification of targeted peptides is achieved using the intensity ratio of a native peptide to the corresponding reference peptide whose spike‐in amount is known. However, a manual calculation of the ratios can be time‐consuming and labor‐intensive, especially when the number of peptides to be tested is large. To establish a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (LC/MALDI TOF/TOF)‐based targeted quantitative proteomics pipeline, we have developed a software named Mass Spectrometry based Quantification (MSQ). This software can be used to automate the quantification and identification of targeted peptides/proteins by the MALDI TOF/TOF platform. MSQ was applied to the detection of a selected group of targeted peptides in pooled human cerebrospinal spinal fluid (CSF) from patients with Alzheimer's disease (AD) in comparison with age‐matched control (OC). The results for the automated quantification and identification of targeted peptides/proteins in CSF were in good agreement with results calculated manually. Copyright © 2010 John Wiley & Sons, Ltd.     

基于海藻酸钠衍生物的肝靶向纳米前药的构建及抗肿瘤活性研究

利用寡聚乙二醇(mOEG)修饰海藻酸钠(ALG), 有效降低了ALG的黏度, 提高了其对疏水性肝靶向配体甘草次酸(GA)的负载量. 结果表明, 靶向材料(GA-ALG-mOEG)的GA负载量为11.8%, 是对照组(GA-ALG)的1.97倍. 在此基础上, 以物理交联的方式引入pH响应的阿霉素前药(DOX-ALG-mOEG), 制备了肝靶向纳米前药(DOX-ALG-mOEG/GA-ALG-mOEG NPs). 细胞实验及抑瘤实验结果表明, 该前药较对照组(DOX-ALG/GA-ALG NPs)具有更高的肝靶向性和药物利用率, 其对肝癌细胞的半致死率浓度(IC₅₀)为58.1 ng/mL, 是对照组(IC₅₀=141.7 ng/mL)的41%; 动物实验结果显示, 该前药的抑瘤率达到了88.4%, 比对照组提高了11.5%.     

Characterization of Cabernet Sauvignon Wines by Untargeted HS-SPME GC-QTOF-MS

Untargeted metabolomics approaches are emerging as powerful tools for the quality evaluation and authenticity of food and beverages and have been applied to wine science. However, most fail to report the method validation, quality assurance and/or quality control applied, as well as the assessment through the metabolomics-methodology pipeline. Knowledge of Mexican viticulture, enology and wine science remains scarce, thus untargeted metabolomics approaches arise as a suitable tool. The aim of this study is to validate an untargeted HS-SPME-GC-qTOF/MS method, with attention to data processing to characterize Cabernet Sauvignon wines from two vineyards and two vintages. Validation parameters for targeted methods are applied in conjunction with the development of a recursive analysis of data. The combination of some parameters for targeted studies (repeatability and reproducibility < 20% RSD; linearity > 0.99; retention-time reproducibility < 0.5% RSD; match-identification factor < 2.0% RSD) with recursive analysis of data (101 entities detected) warrants that both chromatographic and spectrometry-processing data were under control and provided high-quality results, which in turn differentiate wine samples according to site and vintage. It also shows potential biomarkers that can be identified. This is a step forward in the pursuit of Mexican wine characterization that could be used as an authentication tool.     

On-Line HPLC-UV-mass spectrometry and tandem mass spectrometry for the rapid delineation and characterization of differences in complex mixtures: a case study using toxic oil variants

An integrated differential approach to the characterization of complex mixtures is presented which includes the targeting of liquid chromatography (LC) peaks for identification using characteristic UV adsorption of the LC peak, subsequent molecular weight and formula determination using accurate mass LC mass spectrometry (MS), and structure characterization using accurate mass LC-tandem mass spectrometry. The use of differential UV adsorption aids in narrowing the scope of the study to only specific peaks of interest. Accurate mass measurement of the molecular ion species provides molecular weight information as well as atomic composition information. The tandem MS (MS/MS) spectra provide fragmentation information which allows for structural characterization of each component. Accurate mass assignment of each of the fragment ions in the MS/MS spectrum provides atomic composition for each of the fragment ions and thus further aids in the structural characterization. These experiments are facilitated through the use of on-line LC-MS and LC-MS/MS with in-line UV detection. A synthetic toxic oil (STO) related to Toxic Oil Syndrome is studied with a focus on possible contaminants resulting from the interaction of aniline, used as a denaturant, with the normal components of the oil. A differential analysis between the STO and a control oil is performed. LC peaks were targeted using UV absorbance to indicate the possible presence of the aniline moiety. Further differential analysis was performed through the determination of the MS signals associated with each component separated on the LC. Finally, the MS/MS data was also used to determine if the fragmentation of the targeted components indicated the presence of aniline. The MS/MS and accurate mass data were used to assign the structures for the targeted components.     

Diagnostic protein discovery using proteolytic peptide targeting and identification

Plasma protein profiling with mass spectrometry is currently being evaluated as a diagnostic tool for cancer and other diseases. These experiments consist of three steps: plasma protein fractionation, analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and comparisons of the MALDI profiles to develop diagnostic fingerprints using bioinformatic techniques. While preliminary results appear promising in small sample groups, the method is limited by the sensitivity of MALDI-MS for intact proteins, the limited mass range of MALDI-MS, and difficulties associated with isolating individual proteins for identification to validate the diagnostic fingerprint. Here we present an alternative and improved method directed toward diagnostic protein discovery, which incorporates proteolytic peptide profiling, bioinformatic targeting of ion signals, and MALDI tandem mass spectrometry (MS/MS) peptide sequencing, rather than fingerprinting. Pancreatic cancer patients, pancreatitis patients, and controls are used as the model system. Profiling peptides after enzymatic digestion improves sensitivity and extends the accessible protein molecular weight range when compared to intact protein profiling. The first step is to extract and fractionate the proteins from plasma. Each fraction is digested with trypsin and subsequently analyzed by MALDI-MS. Rather than using bioinformatic analysis as a pattern-matching technique, peptides are targeted based on the disease to control peak intensity ratios measured in the averages of all mass spectra in each group and t-tests of the intensity of each individual peak. The targeted peptide ion signals are subsequently identified using MALDI-MS/MS in quadrupole-TOF and tandem-TOF instruments. This study found not only the proteins targeted and identified by a previous protein profiling experiment, but also detected additional proteins. These initial results are consistent with the known biology of pancreatic cancer or pancreatitis, but are not specific to those diseases.     

Terahertz-laser control of large amplitude vibrational motion in the sub-one-cycle pulse limit

We investigate the control of state-selective population transfer in the THz spectral range generated by sub-one-cycle pulse excitation. To this end we developed a zero-net-force modification of the optimal control algorithm which allows us to extend the algorithm into the ultrashort pulse domain. By combining the analysis of the control landscapes and that of optimal control theory, we were able to formulate a general mechanism suitable for laser control by ultrashort pulses. The strategy consists of a superposition of two pi-pulses with carrier envelope phases of phi = pi/2. The first pulse is effectively in resonance with the targeted transition, while the second one, fired at around the minimum of the first pulse second lobe, removes leaking to the dipole-coupled background state. To compensate for the pulses ultrashort duration, the carrier frequencies of both pulses are red-shifted from the spectroscopic resonance.     

Design and evaluation of cyclodextrin-based drug formulation

The pharmaceutically useful cyclodextrins (CyDs) are classified into hydrophilic, hydrophobic, and ionic derivatives. Because of the multi-functional characteristics and bioadaptability, these CyDs are capable of alleviating the undesirable properties of drug molecules through the formation of inclusion complexes or the form of CyD/drug conjugates. This review outlines the current application of CyDs in design and evaluation of CyD-based drug formulation, focusing on their ability to enhance the drug absorption across biological barriers, the ability to control the rate and time profiles of drug release, and the ability to deliver a drug to a targeted site.     

Coexisting Cooperative Cognitive Micro‐/Nanorobots

Interaction behaviors are a crucial, distinctive feature of organisms in ecological systems. Inspired by nature, micro‐/nanorobots also show interaction behaviors with a significant number of novel and advanced functionalities. The micro‐/nanoscale size and self‐driven abilities of micro‐/nanorobots have attracted considerable attention for potential applications. The mission of micro‐/nanorobots has evolved from basic mechanical transfer or assistance to a diverse range of complex tasks, such as targeted drug delivery, biosensing, and environmental remediation. Herein, we focus on the interaction behavior of coexisting cooperative cognitive (Tri‐Co) micro‐/nanorobots, summarize recent research, and classify the interactions into three broad types: with the environment, with robot peers, and with human external control.     

Core/shell nanoparticles in biomedical applications

Nanoparticles have several exciting applications in different areas and biomedial field is not an exception of that because of their exciting performance in bioimaging, targeted drug and gene delivery, sensors, and so on. It has been found that among several classes of nanoparticles core/shell is most promising for different biomedical applications because of several advantages over simple nanoparticles. This review highlights the development of core/shell nanoparticles-based biomedical research during approximately past two decades. Applications of different types of core/shell nanoparticles are classified in terms of five major aspects such as bioimaging, biosensor, targeted drug delivery, DNA/RNA interaction, and targeted gene delivery.     

PEGylated anti-MUC1 aptamer-doxorubicin complex for targeted drug delivery to MCF7 breast cancer cells

Targeted drug delivery is especially important in cancer treatment as many anti-cancer drugs are non-specific and highly toxic to both cancer and normal cells. The targeted drug delivery of DOX to the MUC1-expressing breast cancer cell line (MCF7) was obtained using APT as a carrier. Modification of the APT-DOX complex by PEG increases the survivability of the macrophage control (RAW 264.7) by about six-fold as compared to free DOX treatment without significantly affecting the cytotoxicity toward the target cell line. Thus, PEG-APT-DOX is potentially a new therapeutic agent for targeted drug delivery to MUC1-expressing cell lines.     

Recent Aspect of Cyclodextrin-Based Drug Delivery System

The pharmaceutically useful cyclodextrins (CyDs) are classified into hydrophilic, hydrophobic, and ionic derivatives. These CyDs can serve as multi-functional drug carriers, through the formation of inclusion complex or the form of CyD/drug conjugate. In addition, the combined use of different CyDs and/or pharmaceutical excipients is capable of alleviating the undesirable properties of drug molecules, improving efficacy and reducing side effects. This contribution outlines the potential use of CyDs in the design and evaluation of CyD-based drug formulation, focusing on their ability to enhance the drug absorption across biological barriers, the ability to control the rate and time profiles of drug release, and the ability to deliver a drug to targeted site.     

Transitioning from Targeted to Comprehensive Mass Spectrometry Using Genetic Algorithms

Targeted proteomic assays are becoming increasingly popular because of their robust quantitative applications enabled by internal standardization, and they can be routinely executed on high performance mass spectrometry instrumentation. However, these assays are typically limited to 100s of analytes per experiment. Considerable time and effort are often expended in obtaining and preparing samples prior to targeted analyses. It would be highly desirable to detect and quantify 1000s of analytes in such samples using comprehensive mass spectrometry techniques (e.g., SWATH and DIA) while retaining a high degree of quantitative rigor for analytes with matched internal standards. Experimentally, it is facile to port a targeted assay to a comprehensive data acquisition technique. However, data analysis challenges arise from this strategy concerning agreement of results from the targeted and comprehensive approaches. Here, we present the use of genetic algorithms to overcome these challenges in order to configure hybrid targeted/comprehensive MS assays. The genetic algorithms are used to select precursor-to-fragment transitions that maximize the agreement in quantification between the targeted and the comprehensive methods. We find that the algorithm we used provided across-the-board improvement in the quantitative agreement between the targeted assay data and the hybrid comprehensive/targeted assay that we developed, as measured by parameters of linear models fitted to the results. We also found that the algorithm could perform at least as well as an independently-trained mass spectrometrist in accomplishing this task. We hope that this approach will be a useful tool in the development of quantitative approaches for comprehensive proteomics techniques.

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Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing

DNAzymes exhibit high potential as gene silencing agents for therapeutic applications. Such purposes, however, are significantly challenged by the targeted and successful delivery of unmodified DNAzymes into cells with minimal side effects. Here, we set out to formulate and demonstrate a new stimuli-responsive and constrained aptamer/DNAzyme (Apt/Dz) catenane nanostructure for highly specific gene silencing. The rational design of the Apt/Dz catenane nanostructure with the respective integration of the aptamer sequence and the completely closed catenane format enables both the targeted capability and significantly improved nuclease resistance, facilitating the stable and targeted delivery of unmodified Dz into cancer cells. Moreover, the Dz enzymatic activity in the constrained structure can only be conditionally regulated by the specific intracellular mRNA sequences to silence the target gene with highly reduced side effects. Results show that the Apt/Dz catenane nanostructure can effectively inhibit the expression of the target gene and the proliferation of cancer cells with high specificity.

The stimuli-responsive and constrained aptamer/DNAzyme catenane nanostructure enables the targeted delivery of native DNAzymes for highly specific gene silencing.     

Quantification of the 35S promoter in DNA extracts from genetically modified organisms using real-time polymerase chain reaction and specificity assessment on various genetically modified organisms, part I: operating procedure

A highly sensitive quantitative real-time assay targeted on the 35S promoter of a commercial genetically modified organism (GMO) was characterized (sF/sR primers) and developed for an ABI Prism 7700 Sequence Detection System and TaqMan chemistry. The specificity assessment and performance criteria of sF/sR assay were compared to other P35S-targeted published assays. sF/sR primers amplified a 79 base pair DNA sequence located in a part of P35S that is highly conserved among many caulimovirus strains, i.e., this consensus part of CaMV P35S is likely to be present in many GM events. According to the experimental conditions, the absolute limit of detection for Bt176 corn was estimated between 0.2 and 2 copies of equivalent genome (CEG). The limit of quantification was reached below 0.1% Bt176 content. A Cauliflower Mosaic Virus control (CaMV) qualitative assay targeted on the ORF III of the viral genome was also used as a control (primers 3F/3R) to assess the presence of CaMV in plant-derived products. The specificity of this test was assessed on various CaMV strains, including the Figwort Mosaic Virus (FMV) and solanaceous CaMV strains. Considering the performance of sF/sR quantification test, the highly conserved sequence, and the small size of the amplicon, this assay was tested in a collaborative study in order to be proposed as an international standard.     

Targeted tandem mass spectrometry for high-throughput comparative proteomics employing NanoLC-FTICR MS with external ion dissociation

Targeted tandem mass spectrometry (MS/MS) is an attractive proteomic approach that allows selective identification of peptides exhibiting abundance differences, e.g., between culture conditions and/or diseased states. Herein, we report on a targeted LC-MS/MS capability realized with a hybrid quadrupole-7 tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer that provides data-dependent ion selection, accumulation, and dissociation external to the ICR trap, and a control software that directs intelligent MS/MS target selection based on LC elution time and m/z ratio. We show that the continuous on-the-fly alignment of the LC elution time during the targeted LC-MS/MS experiment, combined with the high mass resolution of FTICR MS, is crucial for accurate selection of targets, whereas high mass measurement accuracy MS/MS data facilitate unambiguous peptide identifications. Identification of a subset of differentially abundant proteins from Shewanella oneidensis grown under suboxic versus aerobic conditions demonstrates the feasibility of such approach.     

Photodynamic Tumor Eradication With a Novel Targetable Photosensitizer: Strong Vascular Effects and Dependence on Treatment Repetition Versus Potentiation

A novel pyropheophorbide‐a (PPa) derivative, Ac‐sPPp, was developed in our lab for targeted photodynamic therapy (PDT) and combination therapies. Its versatile peptide moiety, high water‐solubility, amphiphilicity, and micellar aggregation allow efficient coupling to targeting moieties and convenient mixing with other therapeutics. Photosensitizer immunoconjugate (PIC) targeted PDT, using Ac‐sPPp conjugated to therapeutic anti‐epidermal growth factor receptor (EGFR) antibody cetuximab, and PDT + chemotherapy combination treatment, using Ac‐sPPp mixed with stealth liposomal doxorubicin (Doxil), were investigated as promising strategies for potentiating PDT and improving target specificity. Passively targeted PDT with Ac‐sPPp only or surfactant‐solubilized PPa was also investigated for comparison. The A‐431 human vulvar squamous cell carcinoma, xenografted in nude mice, was chosen as a tumor model because of its high EGFR expression and sensitivity to liposomal doxorubicin in vitro. Fluorescence imaging and PDT experiments showed that Ac‐sPPp formulations circulated far longer and provided superior tumor contrast and superior tumor control compared to PPa. Strong PDT vascular effects were observed by laser Doppler imaging regardless of whether Ac‐sPPp was passively or actively targeted. Passively targeted Ac‐sPPp PDT gave equivalent or better tumor control than PIC‐targeted PDT or PDT + Doxil combination therapy, and when treatments were repeated, it also yielded the highest cure rate.     

手术导航用荧光探针

荧光成像技术因具有操作简便、分辨率高、安全性好且可实时成像等优势,在术中导航中具有广阔的应用前景.虽然目前还没有靶向荧光探针在临床上得到批准,但已经有相当一部分荧光探针进入了临床试验阶段.最早进入临床试验的是一些偶联肿瘤靶向配体的荧光染料,例如近红外菁染料(IRDye800CW)标记的肿瘤特异抗体,叶酸标记的异硫氰酸荧...     

Targeted analysis with benchtop quadrupole–orbitrap hybrid mass spectrometer: Application to determination of synthetic hormones in animal urine

Sensitive and unequivocal determination of analytes/contaminants in complex matrices is a challenge in the field of food safety control. In this study, various acquisition modes (Full MS/AIF, Full MS + tMS/MS, Full MS/dd MS/MS and tSIM/ddMS/MS) and parameters of a quadrupole–orbitrap hybrid mass spectrometer (Q Exactive) were studied in detail. One of the main conclusions has been that, reducing the scan range for Full MS (using the quadrupole) and targeted modes give higher signal-to-noise (S/N) ratios and thereby better detection limits for analytes in matrix. The use of Q Exactive in a complex case, for the confirmatory analysis of hormones in animal urine is presented. A targeted SIM data dependent MS/MS (tSIM/ddMS/MS) acquisition method for determination of eight synthetic hormones (trenbolone, 17α ethinylestradiol, zeranol, stanozolol, dienestrol, diethylstilbestrol, hexestrol, taleranol) and a naturally occurring hormone (zearalenone) in animal urine were optimized to have sensitive precursors from targeted SIM mode and trigger MS/MS scans over the entire chromatograph peak. The method was validated according to EC/657/2002. CCα (decision limit) for the analytes ranged between 0.11 μg L⁻¹ and 0.69 μg L⁻¹ and CCβ (detection capability) ranged between 0.29 μg L⁻¹ and 0.90 μg L⁻¹.     

A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabonomic analysis

Metabonomic/metabolomic studies can involve the analysis of large numbers of samples for the detection of biomarkers and confidence in the analytical data, generated by methods such as GC and HPLC-MS, requires active measures on the part of the analyst. However, quality control for complex multi-component samples such as biofluids, where many of the components of interest in the sample are unknown prior to analysis, poses significant problems. Here the repeat analysis of a pooled sample throughout the run, thereby enabling the analysis to be monitored and controlled using targeted inspection of the data and pattern recognition, is advocated as a pragmatic solution to this problem.