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     

Template-directed porous electrodes in electroanalysis

Nano- and/or macrostructuring of electrode surfaces has recently emerged as a powerful method of improving the performances of electrochemical devices by enhancing both molecular accessibility and rapid mass transport via diffusion, by increasing the electroactive surface area in comparison to the geometric one, and/or by providing confinement platforms for hosting suitable reagents. This brief overview highlights how template technology offers advantages in terms of designing new types of porous electrodes—mostly based on thin films, and functionalized or not—and discusses their use in analytical chemistry via some recent examples from the literature on electrochemical sensors and biosensors.      

Molecular iodine selective membrane for iodate determination in salt samples: chemical amplification and preconcentration

A molecular iodine selective membrane has been used for preconcentration of I₂ generated in situ by iodometric reaction of with excess I⁻ in acidic medium (pH 1–2). This iodometric reaction amplifies the iodine content six times resulting in enhancement of analytical response ranging from three times for molecular methods to six times for elemental methods. The chemical conditions of this iodometric reaction were optimized for quantitative generation and subsequent sorption of I₂ in the membrane samples (96 ± 3%). The homogeneous transparent membrane was prepared by immobilizing I₂-complexing polyvinylpyrrolidone (PVP) in the plasticized cellulose triacetate matrix. Four different analytical methods were examined for quantitative determination of in iodized salt samples by preconcentrating it as I₂ in the membrane matrix. These methods were: (1) spectrophotometry of the PVP-I₂ complex formed in the membrane matrix, (2) a radiotracer method using I⁻ tagged with ¹³¹I radiotracer, (3) instrumental neutron activation analysis (INAA), and (4) energy-dispersive X-ray fluorescence (EDXRF) analysis. The contents thus determined in the iodized salt samples by the membrane-based radiotracer method were compared with the total iodine determined in salt samples by epithermal instrumental neutron activation analysis (EINAA). The membrane-based method for iodate determination in salt samples has advantages over conventional analytical methods, for example preconcentration and chemical amplification, and is free from interference from anions. Figure A molecular iodine selective membrane was used for the quantitative preconcentration of I₂ generated in situ by iodometric reaction of with excess I^aˆ’ in acidic medium, which amplifies iodine content six times     

Purity assessment problem in quantitative NMR—impurity resonance overlaps with monitor signal multiplets from stereoisomers

This paper describes the situation that can emerge when the signals to be evaluated in quantitative NMR measurements—so-called “monitor signals”—consist of several resonance lines from the stereoisomers of the analyte in addition to an impurity signal underneath. The monitor signal problem is demonstrated in the purity assessment of two samples of 2-(isopropylamino)-4-(ethylamino)-6-chloro-1,3,5-triazine (atrazine), a common herbizide which served as analyte in a CCQM intercomparison. It is shown that, in DMSO-d₆ solution, a mixture of stereoisomers leads to several individual overlapping singlets, which are further split by spin–spin coupling. A measurement protocol was developed for finding and identifying an impurity that has a signal that is positioned precisely beneath the methyl signal chosen as the monitor signal in one of the samples. Quantitative NMR purity assessment is still possible in this special case, but with higher uncertainty. Electronic Supplementary Material Supplementary material is available for this article at     

A new ICP–TOFMS. Measurement and readout of mass spectra with 30 μs time resolution, applied to in-torch LA–ICP–MS

In-torch LA–ICP–MS was implemented into an in-house-built ICP–TOFMS system. The fast data acquisition capabilities of the new configuration allowed simultaneous multi-element measurement and readout of in-torch LA–ICP–MS signals with 30 μs time resolution. The measurements confirmed previously observed fine structures of in-torch generated signals and provided new insights in the dynamic processes in the plasma on a microsecond time scale. The new setup is described in detail and first figures of merit are given. Figure Time dependent multi element signal after laser ablation in the torch of an ICP-TOFMS instrument     

Quantitative Peptidomics with Five-plex Reductive Methylation labels

Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of ¹³C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach.

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Multiclass analysis of illicit drugs in plasma and oral fluids by LC-MS/MS

An analytical procedure for the simultaneous determination in human plasma and oral fluids of several illicit drugs belonging to different chemical and toxicological classes is presented. Amphetamine, methamphetamine, morphine, 6-monoacetylmorphine, methylenedioxyamphetamine, methylenedioxyethylamphetamine, methylenedioxymethamphetamine, cocaine, benzoylecgonine, tetrahydrocannabinol, carboxytetrahydrocannabinol, ketamine, and phencyclidine have been quantified in real samples using a very rapid sample treatment, basically a protein precipitation. The quantitative analysis was performed by liquid chromatography–tandem mass spectrometry and has been fully validated. All the analytes were detected in positive ionization mode using a TurboIonSpray source, except carboxytetrahydrocannabinol, which was detected in negative ionization mode. The use of a diverter valve between the column and the mass spectrometer allows the preservation of the ion source performances for high-throughput analysis. Figure Diverter system     

Hydrophilic interaction liquid chromatography (HILIC) in proteomics

In proteomics, nanoflow multidimensional chromatography is now the gold standard for the separation of complex mixtures of peptides as generated by in-solution digestion of whole-cell lysates. Ideally, the different stationary phases used in multidimensional chromatography should provide orthogonal separation characteristics. For this reason, the combination of strong cation exchange chromatography (SCX) and reversed-phase (RP) chromatography is the most widely used combination for the separation of peptides. Here, we review the potential of hydrophilic interaction liquid chromatography (HILIC) as a separation tool in the multidimensional separation of peptides in proteomics applications. Recent work has revealed that HILIC may provide an excellent alternative to SCX, possessing several advantages in the area of separation power and targeted analysis of protein post-translational modifications. Figure Artistic impression of the HILIC separation mechanism     

Investigating morphological changes in treated vs. untreated stone building materials by x-ray micro-CT

Calcareous stones have been largely used to build historical buildings. Among these, the calcarenites are usually characterized by a high content of calcite and a high open porosity, which make them very sensitive to the weathering caused by physical and chemical agents. In order to prevent their deterioration and to retard their decay, different protective products—mainly polymers—are applied on the stone artefact surfaces. In this work we apply the methodology tested in a preliminary study to investigate the morphological changes of the internal structure of a biocalcarenite (Lecce stone) by micro x-ray computed tomography (μ-CT). The porosity and other morphological parameters of the rock before and after the conservation treatment were calculated on a significant number of samples. The Student’s t test was applied for statistical comparison. The results reveal that the treatment with Paraloid B72 (PB 72) is homogenously distributed and causes small changes to the natural properties of the rock, whereas the application of a fluoroelastomer (NH) causes an appreciable decrease in porosity and variation in terms of wall thickness distribution, probably resulting from its inhomogeneous distribution. Figure Porosity and other morphological parameters of Lecce stone were investigated by μ-CT: the effect of conservation treatment with fluoroelastomer on wall thickness distribution is illustrated     

Expanding the scope of MS binding assays to low-affinity markers as exemplified for mGAT1

Following a recently developed concept of MS binding assays based on the quantification of a native marker by LC–MS a procedure to study binding of a low-affinity marker in kinetic, saturation, and competition experiments was established. Separation of bound and unbound marker—the most crucial step of the assay—could be effectively achieved by filtration in a 96-well-format. MS binding assays according to this procedure allowed the reliable characterization of NO 711 binding to mGAT1 in presence of physiological NaCl concentrations. Comparing the results obtained in the present study with those from experiments using 1 mol L⁻¹ NaCl in the incubation milieu reveals remarkable differences with respect to the marker’s affinity and kinetics and to the investigated test compound’s potency. Principle of MS binding assays After incubation of a target with a native marker, bound and unbound marker are separated by filtration. Subsequently, the bound native marker is liberated from the target and finally quantified by LC-MS-MS. Dedicated to Prof. Hans-Dietrich Stachel on the occasion of his 80th birthday     

Evaluation of two proteomics technologies used to screen the membrane proteomes of wild-type <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis> and an <Emphasis Type="SmallCaps">L</Emphasis>-lysine-producing strain

The membrane proteomes of a wild-type Corynebacterium glutamicum and an L-lysine-producing strain were quantitatively analyzed by two complementary proteomics techniques—anion exchange chromatography AIEC/SDS-PAGE and 16BAC-PAGE/SDS-PAGE—and the results were compared. Although both techniques allow for the fast screening of differences in protein abundance, AIEC/SDS-PAGE was superior to 16BAC-PAGE/SDS-PAGE with respect to protein separation, it was more suitable for relative protein quantification, and allowed more differentially regulated proteins to be detected (the succinate dehydrogenase complex, an ABC-type cobalamin/Fe³⁺ siderophore transport system, the maltose binding protein, and a subunit of the cytochrome bc-aa₃ supercomplex were upregulated, while a periplasmic component of an ABC-type transporter and an iron-regulated ABC-type transporter were downregulated in the producer). The results indicate the important role of tricarboxylic acid cycle enzymes as well as the adaptation of transport processes in L-lysine-producing cells. Since the only genetic differences between the wild type and the L-lysine producer occur between four central metabolic enzymes in the cytoplasm, our study illustrates the complex effects of metabolic engineering on cell physiology and the power of the new AIEC/SDS-PAGE proteomics approach to detect these effects.      

Headspace mass spectrometry methodology: application to oil spill identification in soils

In the present work we report the results obtained with a methodology based on direct coupling of a headspace generator to a mass spectrometer for the identification of different types of petroleum crudes in polluted soils. With no prior treatment, the samples are subjected to the headspace generation process and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of volatiles in the sample analysed. The mass spectrum corresponding to the mass/charge ratios (m/z) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. The signals obtained for the different samples were treated by chemometric techniques to obtain the desired information. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required. The method is rapid, simple and, in view of the results, highly promising for the implementation of a new approach for oil spill identification in soils. Figure PCA score plots illustrate clear discrimination of types of crude oil in polluted soil samples (e.g. results are shown for vertisol)     

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.      

Determining sulfamonomethoxine and its acetyl/hydroxyl metabolites in chicken plasma under organic solvent-free conditions

A quantitative technique is described for a sample preparation followed by high performance liquid chromatography method for the simultaneous determination of sulfamonomethoxine and its metabolites, N ⁴-acetyl SMM and 2,6-dihydroxy SMM, in chicken plasma. The average recoveries, analytical total time, and limits of quantitation were ≥80% (relative standard deviations (SD) ≤6%), <30 min sample-1 (12 samples in 2 h), and ≤0.09 μg ml⁻¹, respectively. The procedure, performed under 100% aqueous conditions, uses no organic solvents and toxic reagents at all and is, therefore, harmless to the environment and humans.      

Analysis of biosensors by chemically specific optical techniques. Chemiluminescence-imaging and infrared spectroscopic mapping ellipsometry

The standard methods currently used to read out microarrays are fluorescent and chemiluminesent imaging techniques. These methods require labeling of a component with a marker and, usually, only the concentration of the marker molecule is detected. A label-free imaging method that also enables quantitative spectroscopic analysis of the composition and component interaction would be of great advantage. In this article it is shown for the first time that IR mapping ellipsometry enables label-free imaging of a biochip before and after incubation with peptide solution. The measurements prove that IR ellipsometry is a sensitive tool for laterally resolved identification of the different materials and determination of the composition of a biochip. The lateral resolution required was achieved by using radiation from an infrared synchrotron beamline.      

Rapid response behavior,at room temperature,of a nanofiber-structured TiO<Subscript>2</Subscript> sensor to selected simulant chemical-warfare agents

A chemical prototype sensor was constructed based on nanofiber-structured TiO₂ and highly sensitive quartz resonators. The gas-sensing behavior of this new sensor to selected simulant warfare agents was investigated at room temperature. Results showed rapid response and good reversibility of this sensor when used with high-purity nitrogen. This provides a simple approach to preparation of materials needed as chemical sensors for selected organic volatiles or warfare agents. Figure Sensing behavior of TiO₂ nanofiber sensor to chemical vapors     

A chemoenzymatic synthesis of 3,4,5,6-tetrahydro-2H-benzo[b][1,4]-oxazocine-3,5-dione and its derivatives

Abstract  The enzymatic cyclization of phenoxyacetylcyanomethylenetriphenylphosphorane derivatives using pre-treated baker’s yeast cells, a rapid one-pot assembly of heteromacrocyclic compounds, is described. Graphical abstract        

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     

Determination of IGF-I in horse plasma by LC electrospray ionisation mass spectrometry

The insulin-like-growth factor (IGF-I) peptide is considered to be the main indirect marker for growth hormone administration (GH) in a horse. Further to a previous investigation on measurement of IGF-I in plasma samples by mass spectrometry, this study focuses on quantitative and qualitative analysis of intact IGF-I in horse plasma. First, protein-transposing software has been developed for IGF-I to facilitate its quantification by HPLC–electrospray–ion-trap mass spectrometry. Second, product-ion scan experiments on IGF-I have been conducted on standard samples, non-fortified equine plasma samples, fortified plasma samples, and equine GH post-administration samples. This “top-down” approach method enables characterisation of fragment ions corresponding to the carboxy terminal end, which can be useful for the confirmation of the presence of IGF-I in plasma samples. Figure Structure of IGF-I and amino acid sequences of IGF-I and R3 IGF-I. Deconvolution mass spectra of the IGF-I and R3 IGF-I mixture     

Octadecylsilane-modified silicas in the adsorption of toluene

A series of octadecylsilane-modified silicas were prepared by sol-gel and grafting methods. Carbon contents and octadecyl chain conformations were shown to depend on the preparative route. Grafting engenders a low carbon content and a liquid-like chain conformation, while the sol-gel method affords a much higher carbon content and a crystalline conformation. The relationships between the toluene adsorption of the hybrid silicas and their chain conformations, their carbon contents and their textural characteristics are discussed. These sorbents, when used in combination with ultraviolet diffuse reflectance spectroscopy (UV DRS), can be employed as a rapid screening method for detection of aromatic compounds in water and air environmental matrices. Figure Octadecylsilane-modified silicas in the adsorption of toluene