Playing tag with quantitative proteomics

There is steady need for new proteomic strategies on quantitative measurements that provide essential components for detailing dynamic changes in many cellular functions and processes. Stable isotope labeling is a rapidly evolving field, which can be used either after protein extraction with chemical labeling, or in cell culture with metabolic incorporation. In this review, we explore the most frequently utilized quantitation techniques with particular attention paid to chemical labeling using different isotopic tags, including a recent labeling strategy—soluble polymer-based isotopic labeling (SoPIL)—that achieves efficient labeling in homogeneous conditions. Special care should be devoted to the selection of appropriate quantitation approaches according to the needs of the sample and overall experimental design. We evaluate recent advances in quantitative proteomics using stable isotope labeling and their applications to current insightful biological inquiries. Figure Chemical modules of isotopic tags for quantitative proteomics.     

SPME in environmental analysis

Recent advances in the use of solid-phase microextraction (SPME) in environmental analysis, including fiber coatings, derivatization techniques, and in-tube SPME, are reviewed in this article. Several calibration methods for SPME, including traditional calibration methods, the equilibrium extraction method, the exhaustive extraction method, and several diffusion-based calibration methods, are presented. Recent developed SPME devices for on-site sampling and several applications of SPME in environmental analysis are also introduced.      

Compound-specific stable isotope analysis of organic contaminants in natural environments: a critical review of the state of the art,prospects, and future challenges

Compound-specific stable isotope analysis (CSIA) using gas chromatography-isotope ratio mass spectrometry (GC/IRMS) has developed into a mature analytical method in many application areas over the last decade. This is in particular true for carbon isotope analysis, whereas measurements of the other elements amenable to CSIA (hydrogen, nitrogen, oxygen) are much less routine. In environmental sciences, successful applications to date include (i) the allocation of contaminant sources on a local, regional, and global scale, (ii) the identification and quantification of (bio)transformation reactions on scales ranging from batch experiments to contaminated field sites, and (iii) the characterization of elementary reaction mechanisms that govern product formation. These three application areas are discussed in detail. The investigated spectrum of compounds comprises mainly n-alkanes, monoaromatics such as benzene and toluene, methyl tert-butyl ether (MTBE), polycyclic aromatic hydrocarbons (PAHs), and chlorinated hydrocarbons such as tetrachloromethane, trichloroethylene, and polychlorinated biphenyls (PCBs). Future research directions are primarily set by the state of the art in analytical instrumentation and method development. Approaches to utilize HPLC separation in CSIA, the enhancement of sensitivity of CSIA to allow field investigations in the µg L^–1 range, and the development of methods for CSIA of other elements are reviewed. Furthermore, an alternative scheme to evaluate isotope data is outlined that would enable estimates of position-specific kinetic isotope effects and, thus, allow one to extract mechanistic chemical and biochemical information.Abbreviations BTEX benzene, toluene, ethylbenzene, xylenes - MTBE methyl tert-butyl ether - PAHs polycyclic aromatic hydrocarbons - VOCs volatile compounds - PCBs polychlorinated biphenyls - CSIA compound-specific (stable) isotope (ratio) analysis - GC-IRMS, GC/IRMS or GCIRMS gas chromatography-isotope ratio mass spectrometry - GC-C-IRMS, GC/C/IRMS or GCC-IRMS gas chromatography-combustion-isotope ratio mass spectrometry - irmGC/MS isotope ratio monitoring gas chromatograph-mass spectrometry - GC/P/IRMS gas chromatography-pyrolysis-isotope ratio mass spectrometry (used for D/H) - KIE kinetic isotope effect - PSIA position-specific isotope analysis (for intramolecular isotope distribution) - SNIF-NMR site-specific natural isotopic fractionation by nuclear magnetic resonance spectroscopy     

Current challenges in compound-specific stable isotope analysis of environmental organic contaminants

Compound-specific stable-isotope analysis (CSIA) has greatly facilitated assessment of sources and transformation processes of organic pollutants. Multielement isotope analysis is one of the most promising applications of CSIA because it even enables distinction of different transformation pathways. This review introduces the essential features of continuous-flow isotope-ratio mass spectrometry (IRMS) and highlights current challenges in environmental analysis as exemplified for the isotopes of nitrogen, hydrogen, chlorine, and oxygen. Strategies and recent advances to enable isotopic measurements of polar contaminants, for example pesticides or pharmaceuticals, are discussed with special emphasis on possible solutions for analysis of low concentrations of contaminants in environmental matrices. Finally, we discuss different levels of calibration and referencing and point out the urgent need for compound-specific isotope standards for gas chromatography-isotope-ratio mass spectrometry (GC-IRMS) of organic pollutants.     

Application of Compound-Specific Isotope Analysis in Environmental Forensic and Strategic Management Avenue for Pesticide Residues

Unintended pesticide pollution in soil, crops, and adjacent environments has caused several issues for both pesticide users and consumers. For users, pesticides utilized should provide higher yield and lower persistence while considering both the environment and agricultural products. Most people are concerned that agricultural products expose humans to pesticides accumulating in vegetation. Thus, many countries have guidelines for assessing and managing pesticide pollution, for farming in diverse environments, as all life forms in soil are untargeted to these pesticides. The stable isotope approach has been a useful technique to find the source of organic matter in studies relating to aquatic ecology and environmental sciences since the 1980s. In this study, we discuss commonly used analytical methods using liquid and gas chromatography coupled with isotopic ratio mass spectrometry, as well as the advanced compound-specific isotope analysis (CSIA). CSIA applications are discussed for tracing organic pollutants and understanding chemical reactions (mechanisms) in natural environments. It shows great applicability for the issues on unintended pesticide pollution in several environments with the progress history of isotope application in agricultural and environmental studies. We also suggest future study directions based on the forensic applications of stable isotope analysis to trace pesticides in the environment and crops.     

Determination of antimicrobial residues and metabolites in the aquatic environment by liquid chromatography tandem mass spectrometry

Antimicrobials are used in large quantities in human and veterinary medicine. Their environmental occurrence is of particular concern due to the potential spread and maintenance of bacterial resistance. After intake by the organisms, the unchanged drug and its metabolized forms are excreted and enter wastewater treatment plants where they are mostly incompletely eliminated, and are therefore eventually released into the aquatic environment. The reliable detection of several antimicrobials in different environmental aqueous compartments is the result of great improvements achieved in analytical chemistry. This article provides an overview of the more outstanding analytical methods based on liquid chromatography tandem mass spectrometry, developed and applied to determine antimicrobial residues and metabolites present in surface, waste, and ground waters.      

Novel gel-based rapid test for non-instrumental detection of ochratoxin A in beer

A rapid easy-to-use immunoassay was optimised for the non-instrumental detection of ochratoxin A (OTA) in beer. The analytical method involves preconcentration on the immunoaffinity layer inside a column followed by direct competitive ELISA detection in the same layer. The visual cut-off value, i.e. the lowest OTA concentration resulting in no colour development, was 0.2 μg L^-1. Assay validation was performed using samples spiked with OTA. Thirty-seven naturally contaminated samples were screened with the gel-based method developed and no false-negative results were obtained. The method described offers a simple, rapid and cost-effective screening tool, thus contributing to better health protection of consumers. Figure Gel-based immunoassay of spiked beer samples.     

Accurate quantification of PAHs in water in the presence of dissolved humic acids using isotope dilution mass spectrometry

The effect of dissolved humic acids on the recovery of PAHs from water samples has been investigated using a commercially available humic acid preparation as colloid model and a mixture containing the 16 EPA PAHs. The presence of humic acid reduced the extraction efficiency down to between 10 and 75%. An analytical protocol was therefore developed for the accurate determination of PAHs in the presence of humic acids based on isotope dilution mass spectrometry. The procedure compensates for losses due to sorption of PAHs and can be used for the determination of the total PAH concentration in water, i.e. dissolved PAHs plus PAHs adsorbed on colloids. To obtain reliable estimates it is essential to allow a certain time for equilibration between the isotope spike and the aqueous matrix which may vary between 5 and 24 h, in correlation with the water solubility of PAHs. The protocol allows one to recover the 16 PAHs studied at 94 to 105%. The expanded uncertainty of the measurements was 5–7% for all PAHs. Liquid–liquid extraction and solid-phase extraction in combination with the developed isotope dilution protocol performed equally well for the quantification of PAHs from water samples rich in colloidal material.      

Comparative performance study of different sample introduction techniques for rapid and precise selenium isotope ratio determination using multi-collector inductively coupled plasma mass spectrometry (MC-ICP/MS)

The analytical performance of five sample introduction systems, a cross flow nebulizer spray chamber, two different solvent desolvation systems, a multi-mode sample introduction system (MSIS), and a hydride generation (LI2) system were compared for the determination of Se isotope ratio measurements using multi-collector inductively coupled plasma mass spectrometry (MC-ICP/MS). The optimal operating parameters for obtaining the highest Se signal-to-noise (S/N) ratios and isotope ratio precision for each sample introduction were determined. The hydride generation (LI2) system was identified as the most suitable sample introduction method yielding maximum sensitivity and precision for Se isotope ratio measurement. It provided five times higher S/N ratios for all Se isotopes compared to the MSIS, 20 times the S/N ratios of both desolvation units, and 100 times the S/N ratios produced by the conventional spray chamber sample introduction method. The internal precision achieved for the ⁷⁸Se/⁸²Se ratio at 100 ng mL⁻¹ Se with the spray chamber, two desolvation, MSIS, and the LI2 systems coupled to MC-ICP/MS was 150, 125, 114, 13, and 7 ppm, respectively. Instrument mass bias factors (K) were calculated using an exponential law correction function. Among the five studied sample introduction systems the LI2 showed the lowest mass bias of −0.0265 and the desolvation system showed the largest bias with −0.0321. Figure Illustration of the multi-mode sample introduction system for Se isotope ratiomeasurements     

The role of sulfur and sulfur isotope dilution analysis in quantitative protein analysis

The element sulfur is almost omnipresent in all natural proteomes and plays a key role in protein quantification. Incorporated in the amino acids cysteine and methionine, it has been served as target for many protein-labeling reactions in classic quantitative proteomic approaches based on electrospray or MALDI mass spectrometry. This critical review discusses the potential and limitations of sulfur isotope dilution analysis (IDA) by inductively coupled plasma—mass spectrometry (ICP-MS) for absolute protein quantification. The development of this approach was made possible due to the improved sensitivity and accuracy of sulfur isotope ratio measurement by ICP-MS in recent years. The unique feature of ICP-MS, compound-independent ionization, enables compound (species)-unspecific sulfur IDA. This has the main advantage that only one generic sulfur standard (i.e., one isotopically labeled sulfur spike) is required to quantify each peptide or protein in a sample provided that they are completely separated in chromatography or electrophoresis and that their identities are known. The principles of this approach are illustrated with selected examples from the literature. The discussion includes also related fields of P/S and metal/S ratio measurements for the determination of phosphorylation degrees of proteins and stoichiometries in metalloproteins, respectively. Emerging new areas and future trends such as protein derivatization with metal tags for improved sensitivity of protein detection in ICP-MS are discussed. Figure The key role of sulfur in protein quantification     

Lead isotopic analysis of infant bone tissue dating from the Roman era via multicollector ICP–mass spectrometry

Archaeological samples originating from a cemetery of a Roman settlement, Pretorium Agrippinae (1st–3rd century A.D.), excavated near Valkenburg (The Netherlands) have been subjected to Pb isotopic analysis. The set of samples analysed consisted of infant bone tissue and possible sources of bone lead, such as the surrounding soil, garum, and lead objects (e.g., water pipes). After sample digestion with quantitative Pb recovery and subsequent quantitative and pure isolation of lead, the Pb isotopic composition was determined via multicollector ICP–mass spectrometry. The Pb isotope ratio results allowed distinction of three groups: bone, soil, and lead objects + garum. The ²⁰⁸Pb/²⁰⁶Pb ratio ranges were between 2.059 and 2.081 for the soils, between 2.067 and 2.085 for the bones, and between 2.087 and 2.088 for the lead objects. The garum sample is characterised by a ²⁰⁸Pb/²⁰⁶Pb ratio of 2.085. The bone group is situated on the mixing line between the soil and lead object groups, allowing the statement that diagenesis is not the main cause of the Pb found in the bones.      

Nuclear magnetic resonance of mass-limited samples using small RF coils

Figure Schematic diagram of a typical arrangement used for hyphenating chemical microseparations (e.g. capillary HPLC, CE, or CEC) with microcoil NMR detection     

Application of high-resolution EFTEM SI in an AEM

In this work we show how energy-filtered imaging can be used to obtain spectrum images of electron energy-loss spectrometric data. Focus is placed on improved energy resolution within these data sets. Using two multilayer samples (GaN/AlN and InP/InAs), we demonstrate the advantages of spectrum-imaging and its extended mapping capabilities. Plasmon-ratio maps are used to quickly create high-contrast material maps with high signal-to-noise ratio, ratio-contrast plots are used to gain optimum settings for the ratio maps, and plasmon-position maps are used to map small shifts of the energy position of bulk plasmon peaks. Figure Scheme of EELS SI and derived plasman-position map     

Amplification of noble gas ion lines in the afterglow of a pulsed hollow cathode discharge and possible benefit for analytical glow discharge mass spectrometry

A high-current pulsed hollow cathode discharge was used to study the role of atomic and ionic metastables involved in ionization plasma processes. We observed the enhancement of the spectral emission lines of noble gas ions in the afterglow. A study of the processes that involve atomic and ionic metastables is of great interest since it should lead to a better understanding of and enhanced control over the ionization mechanisms crucial to analytical glow discharge mass spectrometry (GDMS) analysis. Figure Time profile of Ti, Ti⁺, and Ne⁺ spectral lines     

Characterization of imazamox degradation by-products by using liquid chromatography mass spectrometry and high-resolution Fourier transform ion cyclotron resonance mass spectrometry

The photodecomposition of imazamox, a herbicide of the imidazolinone family, was investigated in pure water. The main photoproducts from the photolysis were followed over time by liquid chromatography mass spectrometry and structures were proposed from exact mass determinations obtained by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The method comprised exact mass determination with better than 0.2 ppm mass accuracy and a corresponding structural visualization taking care of respective isotopes with an adapted van Krevelen diagram that enabled a systematic approach to the characterisation of the elementary composition of each photoproduct. By taking advantage of the high resolving power of FT-ICR MS to make precise formula assignments, the derived 2D van Krevelen diagram (O/C; H/C; m/z) enabled one to structurally differentiate the formed photoproducts and to propose a degradation pathway for imazamox. Figure Overview of applied method to analyse the photolysis process of imazamox herbicide     

Fluoroquinolones in soil—risks and challenges

Fluoroquinolones (FQs) are among the most important antibacterial agents used in human and veterinary medicine. Because of the growing practice of adding manure and sewage sludge to agricultural fields these drugs end up in soils, where they can accumulate and have adverse effects on organisms. This paper presents an overview of recent developments in the determination of FQs in solid environmental matrices and describes the risks and challenges (persistence, fate, effects, and remediation) which result from their presence in soil. Figure Pathways into the environment for FQs     

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications. Figure MCR 3: A fully automated chemiluminescence microarray reader for analytical microarrays     

Determination of 13C/12C-ratios of anthropogenic organic contaminants in river water samples by GC-irmMS

This study describes the application of a common analytical procedure adapted for compound-specific stable carbon isotope analyses of riverine contaminants. To evaluate the sensitivity of the analytical method and the precision of the isotopic data obtained, a set of numerous substances at different concentration levels were measured. For most of the anthropogenic contaminants investigated (including chlorinated aliphatics and aromatics, musk fragrances, phthalate-based plasticizers and tetrabutyl tin) acceptable carbon isotope analyses could be obtained down to amounts of approximately 5?ng absolutely applied to the gas chromatograph. These amounts correspond to concentrations in water samples at a natural abundance level of approximately 50–200?ng?L^?1 (low to medium contaminated river systems). However, it has to be considered that the precision and the sensitivity of the analytical method depend partially on the chemical properties of the substances measured. Five recovery experiments were conducted to assess changes in carbon isotope ratios during sample preparation and measurement. The compounds selected for these experiments are known riverine contaminants. Isotopic shifts or higher variations of the isotope ratios as a result of the analytical procedures applied were observed only for a couple of contaminants. Furthermore, compound-specific carbon isotope analyses were performed on eight water extracts of the Rhine river. By comparing the variation of the data of several individual compounds with the deviations obtained from the recovery experiments, it was possible to differentiate contaminants with unaffected isotope ratios and substances with significant alterations of the δ¹³C-values.     

Sensor technology and its application in environmental analysis

Environmental analysis is one of the fundamental applications of chemical sensors. In this review we describe different sensor systems for the gas and liquid phases that have been tested either with real-life samples or in the field during the last five years. Most field sensors rely either on electrochemical or optical transducers. In the gas phase, systems have been proposed for analysis of oxides of nitrogen, carbon, and sulfur in air, and volatile organic compounds. In the liquid phase, most detection systems used for real-life samples detect heavy-metal ions or organic contamination, for example pesticides, organic solvents and polycyclic aromatic hydrocarbons. Figure Chemical sensors for real-life environmental applications Dedicated to Professor Ulrich Nickel on the occasion of his 65th birthday.     

Modì: a new mobile instrument for in situ double-pulse LIBS analysis

Laser-induced breakdown spectroscopy (LIBS) is a promising technique for in situ elemental analysis. A new mobile instrument for LIBS analysis, developed in a collaboration between Marwan Technology s.r.l. and the Applied Laser Spectroscopy Laboratory in Pisa, is presented, and some applications of it and results from it are outlined. The innovative experimental set-up, based on the use of two suitably retarded laser pulses and a standardless analysis procedure, which overcomes problems related to matrix effects, greatly improves the potential of this technique for accurate quantitative analysis.