Multidimensional approaches in biochemical speciation analysis

An understanding of the mechanisms controlling the essentiality and toxicity of trace elements in biological systems at the molecular level depends critically on the possibility of the identification, characterization, and quantification of chemical forms of these elements involved in life processes.Hyphenated techniques based on the combination of (electro)chromatography with ICP MS have become a routine tool for the analysis for metallospecies present in biological tissues. Finer analytical information on the true (down to individual species) speciation of trace elements in living organisms can be obtained by adding additional dimensions to the separation and detection steps, consisting of a sequential use of different HPLC separation mechanisms and capillary electrophoresis at the separation level, and of the use of electrospray MS, including collision induced dissociation MS, on the detection level. The value of the instrumental analytical data is decisively enhanced by the complementary use of molecular biology approaches involving gene identification, cloning and in vitro reproduction of the metal-controlled processes. A brief summary of the recent progress in biochemical speciation analysis is presented in the context of the latest research carried out in the authors' laboratory.     

LC–MS bioanalysis of intact proteins and peptides

Bioanalysis assays that reliably quantify biotherapeutics and biomarkers in biological samples play pivotal roles in drug discovery and development. Liquid chromatography coupled with mass spectrometry (LC–MS), owing to its superior specificity, faster method development and multiplex capability, has evolved as one of the most important platforms for bioanalysis of biotherapeutics, particularly new scaffolds such as half-life extension platforms for proteins and peptides, as well as antibody drug conjugates. Intact LC–MS analysis is orthogonal to bottom-up surrogate peptide approach by providing whole molecule quantitation and high-level sequence and structure information. Here we review the latest development in LC–MS bioanalysis of intact proteins and peptides by summarizing recent publications and discussing the important topics such as the comparison between top-down intact analysis and bottom-up surrogate peptide approach, as well as simultaneous quantitation and catabolite identification. Key bioanalytical issues around intact protein bioanalysis such as sensitivity, data processing strategies, specificity, sample preparation and LC condition are elaborated. For peptides, topics including quantitation of intact peptide vs. digested surrogate peptide, metabolites, sensitivity, LC condition, assay performance, internal standard and sample preparation are discussed.     

DNA‐Templated Copper Nanoprobes: Overview,Feature, Application,and Current Development in Detection Technologies

Metal nanoprobes have recently attracted board research interestinr their application in establishing sensing systems due to their unique optical, electrical, physical, and chemical properties. In comparison to gold and silver nanoprobes, analytical platform based on copper nanoprobes (Cu‐NPs) is still in the early stages of development. In this review, we focus on single‐stranded, and double‐stranded DNA capped Cu‐NPs sensing systems which have been designed for various analytes, including metal ions, anions, small molecules, biomolecules (DNA, RNA, and protein, etc.). In addition, the application of Cu‐NPs in biological labeling or bio‐imaging platforms has also been introduced and summarized.     

Recent advances in capillary electrophoresis‐mass spectrometry: Instrumentation,methodology and applications

Capillary electrophoresis (CE) offers fast and high‐resolution separation of charged analytes from small injection volumes. Coupled to mass spectrometry (MS), it represents a powerful analytical technique providing (exact) mass information and enables molecular characterization based on fragmentation. Although hyphenation of CE and MS is not straightforward, much emphasis has been placed on enabling efficient ionization and user‐friendly coupling. Though several interfaces are now commercially available, research on more efficient and robust interfacing with nano‐electrospray ionization (ESI), matrix‐assisted laser desorption/ionization (MALDI) and inductively coupled plasma mass spectrometry (ICP) continues with considerable results. At the same time, CE‐MS has been used in many fields, predominantly for the analysis of proteins, peptides and metabolites. This review belongs to a series of regularly published articles, summarizing 248 articles covering the time between June 2016 and May 2018. Latest developments on hyphenation of CE with MS as well as instrumental developments such as two‐dimensional separation systems with MS detection are mentioned. Furthermore, applications of various CE‐modes including capillary zone electrophoresis (CZE), nonaqueous capillary electrophoresis (NACE), capillary gel electrophoresis (CGE) and capillary isoelectric focusing (CIEF) coupled to MS in biological, pharmaceutical and environmental research are summarized.     

Investigation of patinas formed on Chinese bronzes using modern multianalytical techniques

This paper presents an integrated study on nine natural Chinese bronze patinas without causing any damage to the bronze substrates, employing five modern analytical techniques including X‐ray diffraction (XRD), Fourier transform infrared (FT‐IR) and Raman spectroscopy, inductively coupled plasma atomic emission spectroscopy (ICP‐AES), and inductively coupled plasma mass spectrometry (ICP‐MS). Two artificial Chinese bronze patinas were also investigated by the same techniques for comparative purposes. As a result, XRD determined the chemical compositions of all selected samples and showed that the primary compound was malachite in natural soil environment under the general situation. Meanwhile, some interesting corrosion products such as gerhardtite and free copper were also observed. Three groups were classified according to the XRD results in order to provide a deeper insight into their spectroscopic characterization. Spectroscopic data of these patinas from FT‐IR and Raman spectroscopy are shown and interpreted in detail. ICP‐AES and ICP‐MS analyses provided valuable quantitative information, and made the study of the patinas more profound. Furthermore, all analytical results indicated that bronze patinas are extremely complex by virtue of the storage environment and their substrate alloys. The natural samples were rather heterogeneous and the artificial samples, especially the sample formed in the laboratory, were rather homogeneous of which the chemical constituents could be well defined. Copyright © 2007 John Wiley & Sons, Ltd.     

Identification and Accurate Size Characterization of Nanoparticles in Complex Media

We have developed a new method for the identification and accurate size characterization of nanoparticles (NPs) in complex media based on capillary electrokinetic (CE) separation coupled to inductively coupled plasma mass spectrometry (ICP‐MS). Through mass scanning and Gaussian fitting of electropherogram peaks, we can obtain multidimensional information on chemical compositions, size distributions, and ionic species of multiple NPs in a single run. The results are more accurate than those obtained by using conventional methods. This method provides a powerful tool for investigating polydisperse NP systems and rapid screening of NP‐containing products.     

Unveiling the rat urinary proteome with three complementary proteomics approaches

Urine is a suitable biological fluid to look for markers of physiological and pathological processes, including renal and nonrenal diseases. In addition, it is an optimal body sample for diagnosis, because it is easily obtained without invasive procedures and can be sampled in large quantities at almost any time. Rats are frequently used as a model to study human diseases, and rat urine has been analyzed to search for disease biomarkers. The normal human urinary proteome has been studied extensively, but the normal rat urinary proteome has not been studied in such depth. In light of this, we were prompted to analyze the normal rat urinary proteome using three complementary proteomics platforms: SDS‐PAGE separation, followed by LC‐ESI‐MS/MS; 2DE, followed by MALDI‐TOF‐TOF and 2D‐liquid chromatography‐chromatofocusing, followed by LC‐ESI‐Q‐TOF. A total of 366 unique proteins were identified, of which only 5.2% of unique proteins were identified jointly by the three proteomics platforms used. This suggests that simultaneous proteomics techniques provide complementary and nonredundant information. Our analysis affords the most extensive rat urinary protein database currently available and this may be useful in the study of renal physiology and in the search for biomarkers related to renal and nonrenal diseases.     

Biological identity of nanomaterials: Opportunities and challenges

The emergence of nanoparticles (NPs) has attracted tremendous interest of the scientific community for decades due to their unique properties and potential applications in diverse areas, including drug delivery and therapy. Many novel NPs have been synthesized and used to reduce drug toxicity, improve bio-availability, prolong circulation time, control drug release, and actively target to desired cells or tissues. However, clinical translation of NPs with the goal of treating particularly challenging diseases, such as cancer, will require a thorough understanding of how the NP properties influence their fate in biological systems, especially in vivo. Many efforts have been paid to studying the interactions and mechanisms of NPs and cells. Unless deliberately designed, the NPs in contact with biological fluids are rapidly covered by a selected group of biomolecules especially proteins to form a corona that interacts with biological systems. In this view, the recent development of NPs in drug delivery and the interactions of NPs with cells and proteins are summarized. By understanding the protein-NP interactions, some guidelines for safety design of NPs, challenges and future perspectives are discussed.     

Low‐molecular‐weight color pI markers to monitor on‐line the peptide focusing process in OFFGEL fractionation

High‐throughput mass spectrometry‐based proteomic analysis requires peptide fractionation to simplify complex biological samples and increase proteome coverage. OFFGEL fractionation technology became a common method to separate peptides or proteins using isoelectric focusing in an immobilized pH gradient. However, the OFFGEL focusing process may be further optimized and controlled in terms of separation time and pI resolution. Here we evaluated OFFGEL technology to separate peptides from different samples in the presence of low‐molecular‐weight (LMW) color pI markers to visualize the focusing process. LMW color pI markers covering a large pH range were added to the peptide mixture before OFFGEL fractionation using a 24‐wells device encompassing the pH range 3–10. We also explored the impact of LMW color pI markers on peptide fractionation labeled previously for iTRAQ. Then, fractionated peptides were separated by RP_HPLC prior to MS analysis using MALDI‐TOF/TOF mass spectrometry in MS and MS/MS modes. Here we report the performance of the peptide focusing process in the presence of LMW color pI markers as on‐line trackers during the OFFGEL process and the possibility to use them as pI controls for peptide focusing. This method improves the workflow for peptide fractionation in a bottom‐up proteomic approach with or without iTRAQ labeling.     

Analysis of diphenylarsinic acid in human and environmental samples by HPLC–ICP‐MS

A simple, rapid and robust analytical method for determining diphenylarsinic acid in human and environmental samples was developed based on a combination of hydrophilic polymer‐based gel‐permeation high‐performance liquid chromatography (HPLC) and inductively coupled plasma mass spectrometry (ICP‐MS). Hair and nail samples were digested with alkali, and liberated diphenylarsinic acid (derivative) was extracted with diethyl ether, redissolved in water and injected for HPLC–ICP‐MS analysis. Human urine, groundwater and water extracts from soils were injected for HPLC–ICP‐MS directly after filtration. Using the method, diphenylarsinic acid in a solution was quantified in 7 min duration for an analysis with a detection limit of sub‐nanograms per milliliter. The method has been applied to groundwater arsenic pollution recently uncovered in Japan. Copyright © 2005 John Wiley & Sons, Ltd.     

Rational strategy for characterization of nanoscale particles by asymmetric-flow field flow fractionation: A tutorial

This tutorial proposes a comprehensive and rational measurement strategy that provides specific guidance for the application of asymmetric-flow field flow fractionation (A4F) to the size-dependent separation and characterization of nanoscale particles (NPs) dispersed in aqueous media. A range of fractionation conditions are considered, and challenging applications, including industrially relevant materials (e.g., metal NPs, asymmetric NPs), are utilized in order to validate and illustrate this approach. We demonstrate that optimization is material dependent and that polystyrene NPs, widely used as a reference standard for retention calibration in A4F, in fact represent a class of materials with unique selectivity, recovery and optimal conditions for fractionation; thus use of these standards to calibrate retention for other materials must be validated a posteriori. We discuss the use and relevance of different detection modalities that can potentially yield multi-dimensional and complementary information on NP systems. We illustrate the fractionation of atomically precise nanoclusters, which are the lower limit of the nanoscale regime. Conversely, we address the upper size limit for normal mode elution in A4F. The protocol for A4F fractionation, including the methods described in the present work is proposed as a standardized strategy to realize interlaboratory comparability and to facilitate the selection and validation of material-specific measurement parameters and conditions. It is intended for both novice and advanced users of this measurement technology.     

Analytical methodologies for aluminium speciation in environmental and biological samples – a review

It is recognized that aluminium (Al) is a potential environmental hazard. Acidic deposition has been linked to increased Al concentrations in natural waters. Elevated levels of Al might have serious consequences for biological communities. Of particular interest is the speciation of Al in aquatic environments, because Al toxicity depends on its forms and concentrations. In this paper, advances in analytical methodologies for Al speciation in environmental and biological samples during the past five years are reviewed. Concerns about the specific problems of Al speciation and highlights of some important methods are elucidated in sections devoted to hybrid techniques (HPLC or FPLC coupled with ET–AAS, ICP– AES, or ICP–MS), flow-injection analysis (FIA), nuclear magnetic resonance (²⁷Al NMR), electrochemical analysis, and computer simulation. More than 130 references are cited.     

Identification of Phototoxic Polycyclic Aromatic Hydrocarbons in Sediments Through Sample Fractionation and QSAR Analysis

Abstract

The toxicity of certain polycyclic aromatic hydrocarbons (PAHs) can be greatly increased by simultaneous exposure of test organisms to ultraviolet (UV) wavelengths present in sunlight. This phenomenon, commonly termed photoinduced toxicity, had been evaluated extensively in laboratory settings where only one chemical of concern was present. However, more recent studies have demonstrated that complex mixtures of PAHs present, for example in sediments, also can cause phototoxicity to a variety of aquatic species when the samples are tested in simulated sunlight. Unfortunately, because these types of samples can contain thousands of substituted and unsubstituted PAHs it is difficult, if not impossible, to use conventional analytical techniques to identify those responsible for photoinduced toxicity. The objective of the present study was to link two powerful ecotoxicology tools, toxicity-based fractionation techniques and QSAR models, to identify phototoxic chemicals in a sediment contaminated with PAHs emanating from an oil refinery. Extensive chromatographic fractionation of pore water from the sediment, in conjunction with toxicity testing, yielded a simplified set of sample fractions containing 12 PAHs that were identified via mass spectroscopy. Evaluation of these compounds using a recently developed QSAR model revealed that, based upon their HOMO-LUMO gap energies, about half were capable of producing photoinduced toxicity. We further evaluated the phototoxic potential of the reduced set of PAHs by determining their propensity to bioaccumulate in test organisms, through calculation of octanol-water partition coefficients for the chemicals. These studies represent a novel linkage of sample fractionation methods with QSAR models for conducting an ecological risk assessment.     

Knowledge discovery in metabolomics: An overview of MS data handling

While metabolomics attempts to comprehensively analyse the small molecules characterising a biological system, MS has been promoted as the gold standard to study the wide chemical diversity and range of concentrations of the metabolome. On the other hand, extracting the relevant information from the overwhelming amount of data generated by modern analytical platforms has become an important issue for knowledge discovery in this research field. The appropriate treatment of such data is therefore of crucial importance in order, for the data, to provide valuable information. The aim of this review is to provide a broad overview of the methodologies developed to handle and process MS metabolomic data, compare the samples and highlight the relevant metabolites, starting from the raw data to the biomarker discovery. As data handling can be further separated into data processing, data pre‐treatment and data analysis, recent advances in each of these steps are detailed separately.     

Joint MS‐based platforms for comprehensive comparison of rat plasma and serum metabolic profiling

Metabolomics is a rapidly growing field in the comprehensive understanding of cellular and organism‐specific responses associated with perturbations induced by medicines, chemicals and environment. Blood matrices are frequently used in clinical and biological studies. In this study, we compared metabolic profiling between rat plasma and serum using complementary platforms of gas chromatography–mass spectrometry (GC‐MS) and liquid chromatography–quadruple time‐of‐flight–mass spectrometry (LC‐QTOF‐MS). The sample types that were tested included plasma prepared with K₂EDTA and serum collected using venous blood collection protocols. The results of peak area variation for each detected metabolite/feature in the quality control samples showed a good reproducibility in LC‐QTOF‐MS and better reproducibility in GC‐MS. In GC‐MS analysis: (a) 25.8% of the defined metabolites differed serum from plasma profiling (t‐test, p < 0.05); and (b) serum possessed higher sensitivity than plasma for its generally higher peak intensity in the metabolic profiling. In LC‐QTOF‐MS analysis, 13 (in positive ion mode) and seven (in negative ion mode) important metabolites were identified as mainly contributing to the separation between serum and plasma. Copyright © 2014 John Wiley & Sons, Ltd.     

Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metalloproteomics and heteroatom-tagged proteomics and metabolomics

The recent developments in analytical techniques capable of providing information on the identity and quantity of heteroatom-containing biomolecules are critically discussed. Particular attention is paid to the emerging areas of bioinorganic analysis including: (i) a comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type (metallomics), (ii) the study of the part of the metallome involving the protein ligands (metalloproteomics), and (iii) the use of a heteroelement, naturally present in a protein or introduced in a tag added by means of derivatisation, for the spotting and quantification of proteins (heteroatom-tagged proteomics). Inductively coupled plasma mass spectrometry (ICP MS), used as detector in chromatography and electrophoresis, and supported by electrospray and MALDI MS, appears as the linchpin analytical technique for these emerging areas. This review focuses on the recent advances in ICP MS in biological speciation analysis including sensitive detection of non-metals, especially of sulfur and phosphorus, couplings to capillary and nanoflow HPLC and capillary electrophoresis, laser ablation ICP MS detection of proteins in gel electrophoresis, and isotope dilution quantification of biomolecules. The paper can be considered as a followup of a previous review by the author on a similar topic (J. Szpunar, Analyst, 2000, 125, 963).     

Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications

In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)‐based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS‐based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow‐up. Copyright © 2016 John Wiley & Sons, Ltd.     

Evaluation of peptide fractionation strategies used in proteome analysis

Peptide fractionation is extremely important for the comprehensive analysis of complex protein mixtures. Although a few comparisons of the relative separation efficiencies of 2‐D methodologies using complex biological samples have appeared, a systematic evaluation was conducted in this study. Four different fractionation methods, namely strong‐cation exchange, hydrophilic interaction chromatography, alkaline‐RP and solution isoelectric focusing, which can be used prior to LC‐MS/MS analysis, were compared. Strong‐cation exchange × RPLC was used after desalting the sample; significantly more proteins were identified, compared with the nondesalted sample (1990 and 1375). We also found that the use of a combination of analytical methods resulted in a dramatic increase in the number of unique peptides that could be identified, compared with only a small increase in protein levels. The increased number of distinct peptides that can be identified is especially beneficial, not only for unequivocally identifying proteins but also for proteomic studies involving posttranslational modifications and peptide‐based quantification approaches using stable isotope labeling. The identification and quantification of more peptides per protein provide valuable information that improves both the quantification of, and confidence of protein identification.     

Speciation Analysis of Thallium by Reversed‐phase Liquid Chromatography ‐ Inductively Coupled Plasma Mass Spectrometry

An inductively coupled plasma mass spectrometer (ICP‐MS) was used as a liquid chromatographic detector for the speciation analysis of thallium in environmental samples. In this study, ionic thallium species, namely Tl(I) and Tl(III) were well separated by reversed‐phase high performance liquid chromatography (RP‐HPLC) with a C8‐HPLC column as the stationary phase and 1 mmol L^?1 tetrabutylammonium phosphate (TBAP), 2 mmol L^?1 diethylenetriamine pentaacetic acid (DTPA) in 1% v/v methanol solution (pH 6) as the mobile phase. Effluent from the HPLC column was delivered to the nebulizer of the ICP‐MS for the determination of thallium. The separation was complete in less than 3 min. Detection limit was 0.002 μg L^?1 for both Tl(I) and Tl(III) compounds based on peak height. The relative standard deviation of the peak areas for five injections of a mixture containing 1 μg Tl L^?1 was better than 3.4%. The concentrations of Tl compounds were determined in standard reference materials, including NIST SRM 1643e Trace Elements in Water and NRCC NASS‐5 Open Ocean Seawater and water samples collected in Kaohsiung area, Taiwan. The HPLC‐ICP‐MS results of the reference samples agreed with the reference values. This method has also been applied to determine Tl(I) and Tl(III) compounds in custard apple (Annona squamosa) leaves collected from Chai‐shan Mountain, Kaohsiung and Taitung City, Taiwan. The thallium species were quantitatively leached from the leaves with a 5 mmol L^?1 DTPA in 100 mmol L^?1 ammonium acetate solution in an ultrasonic bath during a period of 30 min. The HPLC‐ICP‐MS result that was obtained after the analysis of leaves sample showed a satisfactory agreement with the total thallium concentration obtained by ICP‐MS analysis of completely dissolved sample.