Development of a rapid quantitative method of analysis of carbohydrate fatty acid ester reaction mixtures using 1H qNMR

Two new analytical methods, applying absolute 1H qNMR, were developed to monitor product yield and quantify unreacted carbohydrate and fatty acid reactants, in the synthesis of carbohydrate fatty acid esters (CFAE). These methods provide a mass balance of the crude reaction mixtures and diversify the analytical screening and quantitation approaches available within the synthesis of these molecules. Both methods were validated for the model reaction of methyl α-d-glucopyranoside (MAG) and lauric acid (LA) to form the mono ester product, methyl 6-O-dodecanoyl-α-d-glucopyranoside. Analysis in CD3OD by 1H qNMR, with fumaric acid (FA) as an internal standard (IS), allowed monitoring of all reaction components. Alternatively, using CDCl3 and (E)-stilbene as IS enabled the analysis of CFAE and fatty acid. Parameters calculated for method validation included specificity and selectivity, linearity, accuracy, intermediate precision, limit of detection (LOD), limit of quantification (LOQ) and robustness. Both methods provided excellent linearity with R2 > 0.997. The accuracy, precision, and robustness of the method in CD3OD was <2 % uncertainty making it suitable for complete reaction analysis. The method completed in CDCl3 resulted in accuracy, intermediate precision, and robustness of <5 %, except for accuracy in the lowest levels of concentration (>5 %). For all related analytes in the CD3OD and CDCl3 methods, the LOD and LOQ were determined to ensure applicability for the intended use in the assessment of reaction crude composition. Finally, the system suitability was assessed in a scaled lipase catalysed CFAE synthetic reaction. The determined qNMR product yields were verified against isolated purified product yields with <5 % uncertainty.

Synergistic enhancement mediated sensitive SERS-based immunoassay of PSA using versatile PDMS@AgNPs@ZIF-67 biomimetic substrates

Among various biomimetic polymer materials, polydimethylsiloxane (PDMS) stands out as an ideal matrix for surface-enhanced Raman scattering (SERS) due to its unique intrinsic Raman signal and tenacity. In order to realize the precise detection of prostate-specific antigen (PSA), we proposed a sandwich-type SERS-active immunostructure composed of PDMS@silver nanoparticles (Ag NPs)@ZIF-67 biomimetic film as the immunosubstrate and gold nanorods (Au NRs) as immunoprobes. Due to the synergistic effect of electromagnetic enhancement facilitated by biomimetic surfaces and chemical enhancement achieved by ZIF-67, this structure enabled an ultrasensitive and selective detection of PSA across a broad range from 10-3 to 10-9 mg/mL. The achieved limit of detection was as low as 3.0 × 10-10 mg/mL. Particularly, the intrinsic Raman signal of PDMS matrix at 2905 cm-1 was employed as a potential internal standard (IS) in the detection, achieving a high coefficient of determination (R2) value of 0.996. This multifunctional SERS substrate-mediated immunoassay holds vast potential for early diagnosis of prostate cancer, offering promising prospects for clinical applications.

Realization of qualitative to semi-quantitative trace detection via SERS-ICA based on internal standard method

Surface-enhanced Raman spectroscopy (SERS) can quickly identify molecular fingerprints and has been widely used in the field of rapid detection. However, the non-uniformity inherent in SERS substrate signals, coupled with the finite nature of the detection object, significantly hampers the advancement of SERS. Nowadays, the existing mature immunochromatographic assay (ICA) method is usually combined with SERS technology to address the defects of SERS detection. Nevertheless, the porous structure of the strip will also affect the signal uniformity during detection. Obviously, a method using SERS-ICA is needed to effectively solve signal fluctuations, improve detection accuracy, and has certain versatility. This paper introduces an internal standard method combining deep learning to predict and process Raman data. Based on the signal fluctuation of single-antigen SERS-ICA test strip, the double-antigen SERS-ICA test strip was constructed. The full spectrum Raman data of double-antigen SERS-ICA test strip was normalized by the sum of two characteristic peaks of internal standard molecules, and then processed by deep learning algorithm. The Relative Standard Deviation (RSD) of Raman data of bisphenol A was compared before and after internal standard normalization of double-antigen SERS-ICA test strip. The RSD processed by this method was increased by 3.8 times. After normalization, the prediction accuracy of Root Mean Square Error (RMSE) is improved by 2.66 times, and the prediction accuracy of R-square (R2) is increased from 0.961 to 0.994. The results showed that RMSE and R2 were used to comprehensively predict the collected data of double-antigen SERS-ICA test strip, which could effectively improve the prediction accuracy. The internal standard algorithm can effectively solve the challenges of uneven hot spots and poor signal reproducibility on the test strip to a certain extent, so as to improve the semi-quantitative accuracy.

Biomimetic SERS substrate with silicon-mediated internal standard: Improved sensing of environmental pollutants and nutrients

Biomimetic materials with fascinating natural micro-nano surface structures offer a good choice for the simple fabrication of surface-enhanced Raman scattering (SERS) substrate. This study presented a novel sodium carboxymethylcellulose (NaCMC)-Ag biomimetic substrate which was fabricated through the reverse replication of micro-nano structures from cantaloupe peel. Particularly, silicon nanoparticles (Si NPs) were doped into this flexible biomimetic substrate in its fabrication process. Abundant electromagnetic "hotspots" could be effectively excited in this Ag densely covered matrix which maintained numerous protrusions as well as vertical and horizontal grooves. Specifically, the doped Si NPs exhibited a robust intrinsic Raman peak, which could be employed as an internal standard to calibrate the target signal. In this regard, the biomimetic substrate with the optimal electromagnetic enhancement and the quantitative calibration capabilities exhibited a high enhancement factor and a remedied linear relationship in the detection. After a perfect uniformity of signal was proved by the corrected SERS mapping, the biomimetic SERS substrate was finally utilized in the practical analysis of methylene blue (MB) and β-carotene with ultra-low limit of detection, highlighting its importance in practical detection scenarios.

3D hierarchic interfacial assembly of Au nanocage@Au along with IS-AgMNPs for simultaneous, ultrasensitive, reliable, and quantitative SERS detection of colorectal cancer related miRNAs

Simultaneous, reliable, and ultra-sensitive analysis of promising miRNA biomarkers of colorectal cancer (CRC) in serum is critical for early diagnosis and prognosis of CRC. In this work, we proposed a novel 3D hierarchic assembly clusters-based SERS strategy with dual enrichment and enhancement designed for the ultrasensitive and quantitative analysis of two upregulated CRC-related miRNAs (miR-21 and miR-31). The biosensor contains the following: (1) SERS probe, Au nanocage@Au nanoparticles (AuNC@Au NPs) labeled with Raman reporters (RaRs). (2) magnetic capture unit, Ag-coated Fe3O4 magnetic nanoparticles (AgMNPs) modified with internal standard (IS). (3) signal amplify probes (SA probes) for the formation of hierarchic assembly clusters. Based on this sensing strategy, the intensity ratio IRaRs/IIS with Lg miRNAs presents a wide linear range (10 aM-100 pM) with a limit of detection of 3.46 aM for miR-21, 6.49 aM for miR-31, respectively. Moreover, the biosensor shows good specificity and anti-interference ability, and the reliability and repeatability of the strategy were then verified by practical detection of clinical serum. Finally, the biosensor can distinguish CRC cancer subjects from normal ones and guide the distinct tumor, lymph node, and metastasis (TNM) stages. Overall, benefiting from the face-to-face coupling of hierarchic assembly clusters, rapid magnetic enrichment and IS signal calibration of AgMNPs, the established biosensor achieves ultra-sensitive and simultaneous detection of dual miRNAs and opens potential avenues for prediction and staging of CRC.

Robust and sensitive determination of nitrites in pickled food by surface-enhanced Raman spectroscopy

Nitrites are ubiquitous in food and pose a serious threat to human health. Therefore, the rapid and accurate determination of nitrite ion concentration in food is a prerequisite for eliminating the damage of nitrites. In this study, a robust, rapid, and sensitive method is proposed for nitrite detection in pickled food, in which Au@Ag nanoparticles are used as a reliable surface-enhanced Raman spectroscopy (SERS) substrate taking advantage of the high enhancement effect of silver and the good stability of gold. Nitrites were anchored to the surface of the SERS substrate by bridging with 4-aminophenylthiophenol (PATP). With Raman scattering cross-section amplification and internal calibration by PATP, a satisfactory linear relationship (R2 = 0.987) was established for nitrite detection in the concentration range of 5.00-100.00 μM, and the limit of detection (LOD) was 0.17 μM. This SERS-based method demonstrated high selectivity, good precision (RSD < 7.00 %), and satisfying recovery rates (101.42-107.35 %) in real samples, thus improving the determination method for nitrites. Therefore, this method has application potential in food safety and supervision.

SERS-active immunoassay kit for SARS-CoV‑2 mediated by the cooperative chemical and electromagnetic effects of MXene modified with gold nanowires

Surface-enhanced Raman scattering (SERS) technique with high sensitivity, reliable specificity, and rapid recognition ability exhibits attractive promise for the effective fast-monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, a novel SERS-active immunoassay kit for SARS-CoV-2 nucleocapsid (N) protein was prepared by in-situ growing gold (Au) nanowire forests (NFs) onto Ti3C2Tx, which was then modified onto polymethyl methacrylate (PMMA) matrix and encapsulated into kit. It was noted that the Au nanowires with fibrous structures which vertically anchored on Ti3C2Tx served as perfect channels to promote photo-induced charge transfer. The synergistic action of electromagnetic and chemical effects resulted in an enhancement factor (EF) of 1.27 × 107. Furthermore, the unreliable fluctuation of the enhanced signal was eliminated by using the intrinsic Raman signal of the flexible PMMA platform, achieving an improved correlation coefficient (R2) value from 0.950 to 0.990. Moreover, the as-designed immunoassay kit with both high sensitivity and remedied quantitative ability rendered by the Ti3C2Tx@Au NFs-PMMA composite exhibited a powerful performance in the practical detection of N-protein with concentration low to 5.0 × 10-8 mg/mL.

Comparison of calibration strategies for accurate quantitation by isotope dilution mass spectrometry: a case study of ochratoxin A in flour

Analysis of low-level organic contaminants in complex matrices is essential for monitoring global food safety. However, balancing sample throughput with complex experimental designs and/or sample clean-up to best reduce matrix effects is a constant challenge. Multiple strategies exist to mitigate these effects, with internal standard-based methods such as isotope dilution mass spectrometry (IDMS) being the most advantageous. Here, multiple internal calibration strategies were investigated for the quantification of ochratoxin A (OTA) in wheat samples by liquid chromatography-mass spectrometry (LC-MS). Internal standard-based quantitation methods such as single (ID1MS), double (ID2MS), and quintuple (ID5MS) isotope dilution mass spectrometry, as well as external standard calibration, were explored and compared. A certified reference material (CRM) of OTA in flour, MYCO-1, was used to evaluate the accuracy of each method. External calibration generated results 18-38% lower than the certified value for MYCO-1, largely due to matrix suppression effects. Concurrently, consistently lower OTA mass fractions were obtained for the wheat samples upon quantitation by external calibration as opposed to ID1MS, ID2MS, and ID5MS. All isotope dilution methods produced results that fell within the expected range for MYCO-1 (3.17-4.93 µg/kg), validating their accuracy. However, an average 6% decrease in the OTA mass fraction was observed from results obtained by ID1MS compared to those by ID2MS and ID5MS. Upon scrutiny, these differences were attributed to an isotopic enrichment bias in the isotopically labelled internal standard [13C6]-OTA that was used for ID1MS, the OTAL-1 CRM. The advantages and limitations of each isotopic method are illustrated.

Determination of glyphosate and aminomethylphosphonic acid residues in Finnish soils by ultra-high performance liquid chromatography-tandem mass spectrometry

Glyphosate [N-(phosphonomethyl) glycine] (GLY) adsorbs strongly in Finnish soils. A new method for GLY and its main degradation product, aminomethylphosphonic acid (AMPA) residues in clay soils (Protovertic Luvisol) was developed and validated. A new method was necessary because the previous one required laborious cleaning pre-treatments, and its recovery was quite poor (<40%-70%). In the new method, the earlier method's extraction solvent, 0.1 M potassium hydroxide (KOH), was replaced by more effective 0.6 M KOH. The old post-column high-performance liquid chromatography and fluorescence (HPLC-FLD) method was replaced by the ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method. Compounds were identified as their fluorenyl methyl chloroformate (FMOC) derivatives by a multiple reaction monitoring (MRM) technique and quantified by an internal standard method utilising multipoint matrix-matched calibration. Glufosinate-ammonium (GLUF) was used to monitor the effectiveness of extraction with good recovery (80-119%). All calibration curves were found to be linear (R2 ≥ 0.98) in the studied calibration range (0.01-3.31 mg kg-1 in fresh soil). The repeatability and reproducibility were 25% and 28% for GLY, and 20% and 24% for AMPA in real research soil samples. The method was effective throughout the calibration range in all the studied Finnish agricultural soils.•An improved method was created to analyse glyphosate (GLY) and AMPA in Finnish clay soil.•The challenge caused by strong GLY adsorption on soil was solved by using multipoint matrix-matched calibration curve samples which were prepared identically with the research samples.•The method performed well in all tested clay, loam and sandy loam soils.

A core-molecule-shell Au@PATP@Ag nanorod for nicotine detection based on surface-enhanced Raman scattering technology

Nicotine is an addictive substance often found in tobacco and cigarette smoke and excessive exposure to it can cause various diseases. Herein, core-molecule-shell gold/4-aminothiophenol/silver nanorods (Au@PATP@Ag NRs) were prepared for quantitative detection of nicotine by using surface-enhanced Raman scattering (SERS) technology. The obtained Au@PATP@Ag NRs showed an outstanding SERS effect due to the plasticity of their morphology and the bimetallic synergistic effect between the excellent stability of Au and the highly enhanced effect of Ag. The Au@PATP@Ag NRs substrate exhibited an extremely high enhancement factor (EF) of 2.17 × 107. In addition, in-situ synthesized PATP was used as an internal standard to correct signal fluctuation and improve the reliability of quantitative nicotine detection. A wide linear dynamic range from 10-8 to 10-3 M was obtained and an ultra-low limit of detection (LOD) was about 3.12 × 10-9 M, which was superior to most of previously reported methods. This work has also been used for determining nicotine content in cigarettes and simulated environmental tobacco smoke by using a portable device. These results indicated that the developed SERS method had many potential applications in the quantitative determination of nicotine in real tobacco samples.

Can plant hormonomics be built on simple analysis? A review

The field of plant hormonomics focuses on the qualitative and quantitative analysis of the hormone complement in plant samples, akin to other omics sciences. Plant hormones, alongside primary and secondary metabolites, govern vital processes throughout a plant's lifecycle. While active hormones have received significant attention, studying all related compounds provides valuable insights into internal processes. Conventional single-class plant hormone analysis employs thorough sample purification, short analysis and triple quadrupole tandem mass spectrometry. Conversely, comprehensive hormonomics analysis necessitates minimal purification, robust and efficient separation and better-performing mass spectrometry instruments. This review summarizes the current status of plant hormone analysis methods, focusing on sample preparation, advances in chromatographic separation and mass spectrometric detection, including a discussion on internal standard selection and the potential of derivatization. Moreover, current approaches for assessing the spatiotemporal distribution are evaluated. The review touches on the legitimacy of the term plant hormonomics by exploring the current status of methods and outlining possible future trends.

A pH-responsive sensor based on intramolecular internal standard for reproducible detection of strong acids and bases via 19F NMR spectroscopy

Numerous methods, including pH meters and optical sensors, have been developed for the detection of pH, which is an important indicator in various fields. However, those methods are susceptible to errors in strongly acidic and basic ranges and inaccurate pH measurement due to sample turbidity, hindering their application such as photographic industries and wastewater treatment facilities. Eco-friendly and non-invasive ¹⁹F NMR spectroscopy is a promising technique for measurement of strong acids and bases owing to its high sensitivity and little interference; nevertheless, inconsistencies in reproducibility impede its widespread adoption. Herein, we developed a¹⁹F NMR-based pH sensor by introducing an intramolecular internal standard strategy into a pH-responsive fluorinated material. Based on the acceptable deviation (Δδ_F = 17-19 ppb) in the evaluation of the internal standard signal, this pH-sensing platform enabled reproducible pH measurements in strongly acidic and basic environments. Moreover, its ¹⁹F NMR response showed reversibility and high stability to potential interfering factors, and the low absolute difference (0.026-0.086 in pH) for real samples such as diet Coke suggests its potential suitability for various acidic beverages.

Two-dimensional glass/p-ATP/Ag NPs as multifunctional SERS substrates for label-free quantification of uric acid in sweat

Abnormal uric acid (UA) content in body fluids can fully reflect the status of metabolism and immunity in the body. We have developed a simple, efficient and label-free surface enhanced Raman scattering (SERS) method for UA detection. Briefly, p-aminothiophenol (p-ATP) was used as the internal standard molecule and linking molecule to prepare a glass/p-ATP/Ag NPs SERS substrate. The Raman characteristic peak of p-ATP at 1076 cm^-1 can be used as an internal standard molecule to correct the signal fluctuation of UA detection. The results show that the SERS method owns a linear response with a ranging from 5 × 10^-6 to 10^-3 M of UA characteristic peak of both 693 cm^-1 and 493 cm^-1 with a determination coefficient (R²) of 0.9878 and 0.9649, respectively. Additionally, the SERS sensor has been further used for the analysis of UA in sweat and good recoveries were obtained for the sensing of sweat. We believe that the developed SERS substrate has potential for applications in healthcare monitoring.

Opioid cutting agents for use as internal standards in ion mobility spectrometry (IMS)

Opioids have become a serious public health concern over the last decade. These compounds are commonly found mixed, or cut, with safer compounds to make the opioids appear unadulterated while also enhancing the psychoactive effect on the user. Commercial benchtop and handheld IMS devices are capable of detection but published reduced ion mobility (K₀) values, used to identify the target analytes with IMS instrumentation, have shown variability. This lack of agreement, even for compounds used for calibration, is often due to the effects of drift tube temperature, drift gas water vapor levels and the use in-house built instrumentation rather than commercial equipment. Multiple reports exist on assessment of IMS reference standards but a single, consensus universal standard does not exist. Assessment of opioid cutting agents as internal standards is a worthwhile pursuit if precise and accurate K₀ values are obtained. The effects of drift gas water vapor content and drift tube temperature were used to evaluate the cutting agents. The K₀ values of papaverine, a representative opioid with a similar K₀ value to heroin and fentanyl, were calculated with respect to quinine and were in agreement with literature data. The use of quinine as an internal standard also improved precision relative to the instrument standard and shows promise in the application presented here.

Semi-wrapped gold nanoparticles for surface-enhanced Raman scattering detection

Researchers have struggled to develop highly reliable and sensitive surface-enhanced Raman scattering (SERS) substrates for detecting compounds in complicated systems. In this work, a strategy by constructing Au cores with incompletely wrapped Prussian blue (PB) for highly reliable and sensitive SERS substrate is proposed. The wrapped PB layers can provide the internal standard (IS) to calibrate the SERS signal floatation, whereas the exposed surface of Au cores offers the enhancement effect. The balance between the signal self-calibration and enhancement (hence the trade-off between SERS reliability and sensitivity) is obtained by the approximate semi-wrapping configuration of PB layers on Au cores (i.e., SW-Au@PB). The proposed SW-Au@PB nanoparticles (NPs) exhibit the similar enhancement factor as the pristine Au NPs and contribute to the ultralow RSD (8.55%) of calibrated SERS signals using R6G as probe molecules. The simultaneously realized reliability and sensitivity of SW-Au@PB NPs also enables the detection of hazardous pesticide residues such as paraquat and thiram in herbal plants, with the average detection accuracy up to 92%. Overall, this work mainly provides a controllable synthetic strategy for incompletely wrapped NPs, and most importantly, explores the potential with a proof-of-concept practical application in accurate and sensitive Raman detection of hazardous substances with varying solubility.

Optimization of ICP-MS internal standardization for 26 elements by factorial design experiment

INTRODUCTION

Internal standardization is a common tool used in inductively coupled plasma - mass spectrometry (ICP-MS) analysis in order to reduce matrix effects, and thus improve the reliability and the robustness of results. However, its efficacy relies on the choice of a proper internal standard (IS) which, ideally, undergoes the same signal variations as the analyte. Thus far, IS selection has mainly relied on the proximity of atomic mass between the analyte and the internal standard. However, while it may be a satisfactory rule of thumb, more recent works suggest that this criterium might not be suitable in several conditions, among which the presence of high amounts of carbon atoms in the sample. This may thus be of particular interest in the case of trace elements determination in biological samples.

MATERIALS AND METHODS

In this study, we propose an empirical and global approach to IS selection in ICP-MS through the use of a factorial design of experiments (DoE), with a focus on biological matrices of interest in clinical analysis: human blood and urine. The suitability of 13 potential IS was evaluated for 26 clinically-relevant analytes, including a polyatomic ion obtained through reaction with oxygen, across 324 experimental conditions.

RESULTS AND DISCUSSION

The results underline several exceptions to the rule of IS selection based on mass proximity, notably when considering heavy or polyatomic analytes. As a consequence, measurements of said analytes in several extreme experimental conditions using IS selected by mass proximity could yield vastly erroneous results (up to 30 times the theoretical concentrations). By contrast, the use of empirically selected IS yielded much more acceptable results.

Spatially Resolved Quantitation of Drug in Skin Equivalents Using Mass Spectrometry Imaging (MSI)

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has seen a growing interest as a leading technique in the pharmaceutical industry for mapping label-free exogenous and endogenous species in biological tissues. However, the use of MALDI-MSI to perform spatially resolved absolute quantitation of species directly in tissues is still challenging, and robust quantitative mass spectrometry imaging (QMSI) methods need to be developed. In this study, we describe the microspotting technique for analytical and internal standard deposition, matrix sublimation, powerful QMSI software, and mass spectrometry imaging setup to obtain absolute quantitation of drug distribution in 3D skin models.

DIGE Analysis of Animal Tissues

Two-dimensional difference gel electrophoresis (2D-DIGE) is an acrylamide gel electrophoresis-based technique for protein separation and quantification in complex mixtures. The technique addresses some of the drawbacks of conventional 2D polyacrylamide gel electrophoresis (2D-PAGE), offering improved sensitivity, more limited experimental variation, and accurate within-gel matching. 2D-DIGE is based on direct labeling of proteins with isobaric fluorescent dyes (known as CyDyes: Cy2, Cy3, and Cy5) prior to isoelectric focusing (IEF). Here, up to two samples and a reference pool (internal standard) can be mixed and loaded onto IEF for first dimension prior to SDS (sodium dodecyl sulfate)-PAGE separation in the second dimension. After the electrophoretic run, the gel is imaged at the specific excitation wavelength for each dye, in sequence, and gel scans are recorded separately. For each individual protein spot, intensities recorded at the different wavelengths are integrated and the ratio between volumes normalized to that of the internal standard. This provides an immediate appreciation of protein amount variations under the different conditions tested. In addition, proteins of interest can still be excised and identified with conventional mass spectrometric techniques and further analyzed by other biochemical methods. In this chapter, we describe application of this methodology to separation and quantitation of protein mixtures from porcine muscle exudate, collected following centrifugation of muscle specimens (centrifugal drip) for the characterization of quality parameters of importance in meat industry.

Quantitative SERS sensing mediated by internal standard Raman signal from silica nanoparticles in flexible polymer matrix

Attributed to poor signal uniformity and external interference, ultrasensitive surface-enhanced Raman spectroscopy (SERS) still faces difficulties in the reliable and quantitative detection of trace molecules. Here, a facile Ag/Si/sodium carboxy methyl cellulose (NaCMC) film with internal standard (IS) was promoted for quantitative determination of thiram. The effects of preparation conditions on SERS activity of the film were systematically investigated and then a flexible SERS substrate with high sensitivity and uniformity was fabricated. The enhancement factor was calculated to be 1.12 × 10⁶ and SERS mapping was recorded with a relative standard deviation value of 19.8% by utilizing 4-mercaptobenzoic acid (4-MBA) as target molecule. Additionally, the dominant contribution of the IS from encapsulated Si nanoparticles (NPs) was confirmed in the quantitative assay of 4-MBA and thiram, facilitating attractive fitting coefficients (R²) as 0.991 and 0.998. Besides that, the proposed flexible film was conducted to scrub trace thiram from the surfaces of apple, orange, and cucumber, resulting in recoveries of 89%, 94%, and 91%. A smart and facile quantitative SERS substrate was developed here for monitoring trace biochemical molecules, verifying its potential utilizations in monitoring pesticide residues.

Elemental bioimaging of Zn and Cd in leaves of hyperaccumulator Arabidopsis halleri using laser ablation-inductively coupled plasma-mass spectrometry and referencing strategies

The spatial distribution of Zn and Cd in leaves of the heavy metal hyperaccumulator species Arabidopsis halleri, a land plant in the Brassicaceae family of angiosperms, is determined by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Detected intensities of nuclides of the environmental pollutants Zn and Cd are referenced to nuclides of the naturally abundant elements C, Mg, P, Ca, and Rb as internal standards, in order to compensate for widespread experimental issues in whole-leaf laser ablation. Referencing occurs by dividing the signal intensity of the analyte by the corresponding intensity of the internal standard. In order to avoid large quotients that occur during division by small numbers, quotients of pixels for which the internal standard is no higher than the background are set to zero. The effects of referencing on a loss of laser focus, overlapping layers of leaf tissue and cell damage within the imaged leaf tissue are addressed specifically. It is reported that referencing to ²⁵Mg, ³¹P, ⁴⁴Ca or ⁸⁵Rb can skew the results of Zn and Cd distribution because of their different ion mobility within leaves or other element-specific effects. This is particularly valid in the leaf venation and in regions of leaves where cell damage has occurred. Considering all aspects, ¹³C was found to be best suited among the investigated elements for referencing of leaves, because it stabilizes the resulting distributions of Zn and Cd even in samples affected by experimental issues.

Bioinspired surface-enhanced Raman scattering substrate with intrinsic Raman signal for the interactive SERS detection of pesticides residues

Although biomimetic surface enhanced Raman scattering (SERS) substrate which makes use of naturally existing raw materials have been fully utilized, it remains challenging to achieve credible quantitative detection. Herein, nanoimprint technology was exploited to engineer internal standard (IS) enabled quantitative flexible biomimetic SERS substrates, in which polydimethylsiloxane (PDMS) with intrinsic Raman signal was utilized as a tool to reversely duplicate surface structures from different agriculture products and then deposited with Ag nanoparticles. The resultant four kinds of biomimetic SERS substrates with different surface geometries all permit highly sensitive assay with enhancement factors (EFs) of about 10⁶ in both drop-dry and in situ SERS detection modes. Moreover, the quantitative degree in the SERS detection was effectively corrected based on the IS strategy. Finally, an ingenious interactive in situ SERS detection was conducted. Interestingly, the maximum recovery rate was achieved when the template food was used as target surface compared with other foods, indicating the significance of manufacturing the highly conformed SERS-active structure from the surface to be tested. The proposed quantitative biomimetic SERS substrate is expected to be widely used in the field of biochemical supervision.

Development of a comprehensive approach for performance evaluation of a quantitative multi-attribute method as a quality control method

The multi-attribute method has been recognized as an elegant quantification tool for post-translational modifications (PTMs) of therapeutic proteins, since it can evaluate several attributes spontaneously and site-specifically. Here, the abundance of PTMs calculated by three different types of formula were compared and there was little difference among the results. For the method evaluation, two different kinds of peptides were used as internal standards (ISs) and one of the IS was used as the "standard peak" to define the signal strength of MS. They are also used for system suitability testing to verify whether the condition or sensitivity of mass spectrometry are high enough to evaluate the minor components by confirming the recovery rate of one IS to the another. This system is beneficial that since we have defined the limit of quantification as a certain ratio to IS, consistent MS intensity is applied as the threshold across all detected peaks.

Rapid absolute quantification of pathogens and ARGs by nanopore sequencing

Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.

Design and synthesis of a novel ZB716-d6 as a stable isotopically labeled internal standard

ZB716 is a synthetic, steroidal, orally active anti-estrogen agent that is under clinical development for the treatment of estrogen receptor (ER)-positive metastatic breast cancer. The stable isotope-labeled ZB716 was required for use as an internal standard in LC-MS/MS assays. Therefore, a novel deuterated ZB716 (ZB716-d6) as an isotopically labeled internal standard was designed and synthesized through a newly developed route, which prepared ZB716-d6 in eight steps from the commercially available deuterium-labeled starting material [²H₆]pentafluoropentanol. This procedure is very practicable and gives the final compound in good yield (19% total yield) and high purity (D, >99%, chemical purity 98%). At present, ZB716-d6 has been successfully used as an internal standard in clinical bioanalysis.

Functionalization of Magnetic Beads with Biotinylated Nanobodies for MALDI-TOF/MS-Based Quantitation of Small Analytes

Over the last two decades, the variable domains from heavy chain-only antibodies in camelids (nanobodies) have emerged as valuable immunoreagents for analytical and diagnostic applications. One prominent use of nanobodies is for the detection of small molecules due to their ease of production, resistance to solvents used in sample extraction, facile genetic manipulation, and small size. These last two properties make it possible to produce biotinylated nanobodies in vivo, which can be loaded in an orientated manner on magnetic beads covered with avidin, creating high-density immunoadsorbenpi twbch ""ts. The method described here details the use of nanobody-based adsorbents to concentrate small molecular weight analytes for subsequent quantitative analysis by MALDI-TOF mass spectrometry. Quantitation requires the inclusion of an internal standard (IS), a compound with properties similar to those of the analyte, enabling compensation for uneven distribution during crystallization of the MALDI-TOF matrix. Since nanobody generation against small compounds requires conjugation to carrier proteins, the same conjugation chemistry can be used to synthesize the IS. By design the IS cross reacts with the capture nanobody and can be preloaded in the immunoadsorbent, facilitating quantitative detection of the target compound.

Determination of the aqueous pKa of very insoluble drugs by capillary electrophoresis: Internal standards for methanol-water extrapolation

A fast determination of acidity constants (pK_a) of very insoluble drugs has become a necessity in drug discovery process because it often produces molecules that are highly lipophilic and sparingly soluble in water. In this work the high throughput internal standard capillary electrophoresis (IS-CE) method has been adapted to the determination of pK_a of water insoluble compounds by measurement in methanol/aqueous buffer mixtures. For this purpose, the reference pK_a values for a set of 46 acid-base compounds of varied structure (internal standards) have been established in methanol-water mixtures at several solvent composition levels (with a maximum of 40% methanol). The IS-CE method has been successfully applied to seven test drugs of different chemical nature with intrinsic solubilities lower than 10^-6 M. pK_a values have been determined at different methanol/aqueous buffer compositions and afterwards Yasuda-Shedlovsky extrapolation method has been applied to obtain the aqueous pK_a. The obtained results have successfully been compared to literature ones obtained by other methods. It is concluded that the IS-CE method allows the determination of aqueous pK_a values using low proportions of methanol, becoming then more accurate in the extrapolation procedure than other reference methods.

Reliable SERS detection of pesticides with a large-scale self-assembled Au@4-MBA@Ag nanoparticle array

The fabrication of sensitive and reliable interfacial plasmonic platform for measuring chemical contaminants in various phases is an exciting topic in the food industry and for environment monitoring. In this study, a high-performance surface-enhanced Raman spectroscopy (SERS) analytic platform was developed through self-assembly of the gold@4-mercaptobenzoic acid@silver nanoparticles (Au@4-MBA@Ag NPs) at the cyclohexane/water interface. By addition of the inducer ethanol, the Au@4-MBA@Ag NPs in aqueous phase was effectively migrated to the biphasic interface, forming a large-scale close-packed nanoparticle array. The average gap between adjacent nanoparticles was smaller than 3 nm, where intensive SERS "hot spots" were created for high-sensitive detection. Furthermore, using the sandwiched 4-MBA molecule as the internal standard to correct the Raman signal fluctuations, the point-to-point and batch-to-batch reproducibility of Au@4-MBA@Ag array were improved with lower relative standard deviation (RSD) values of 8.84% and 14.97%, respectively, and pesticides (thiram and thiabendazole) analysis in both aqueous and organic phases were achieved with higher accuracy (R² of 0.986 and 0.990) as compared with those without 4-MBA correction (R² of 0.867 and 0.974). The high-throughput fabrication of the self-assembled nanoparticle array is a promising approach for development of a sensitive and reliable SERS platform for chemical contaminants monitoring in multiphase.

Surface-enhanced Raman scattering-based lateral flow immunoassay mediated by hydrophilic-hydrophobic Ag-modified PMMA substrate

Recently, it is urgent to ameliorate the accumulation and quantification performances of surface-enhanced Raman scattering-based lateral flow immunoassay (SERS-based LFIA) to promote its reliable clinical application. Herein, a smart hydrophilic-hydrophobic SERS-based LFIA strip was demonstrated by decorating Ag nanoplates with hydrophilic surface onto the specific regions of hydrophobic polymethylmethacrylate (PMMA) film with Raman internal standard (IS), which can unexpectedly inhibit the "coffee-ring phenomenon". The target analytes were consequently enriched in the SERS-active Ag regions by the hydrophobic PMMA, considerably endowing the strip with amended quantitative monitoring ability. Aided by immunoprobes of flower-shaped Ag nanoplates, a limit of detection as 10 pg/mL and an outstanding correlation coefficient value (R²) of 0.992 for carcinoembryonic antigen (CEA) were obtained by utilizing this SERS-based LFIA strip, which can be conducive to clinical monitoring and will broaden the field of vision for the point-of-care diagnostic technique.

The novel Outer Plug Standardization (OPS) calibration strategy applied in a new method for the high-throughput determination of Cl-, NO3- and SO4-2 in rainwater samples

This paper presents the Outer Plug Standardization - OPS, a novel technique as an alternative for the classic internal standardization using multiple injection in capillary zone electrophoresis is proposed herein. This technique was applied in a new method for the determination of chloride, nitrate and sulfate in rainwater samples. After the injection accuracy was tested and proved to be a minor error source (average 1.26% RSD), the OPS was applied and it improved the intra-day and inter-day precision of the analytical method by 32.5% and 24.7%, respectively. Using a capillary with effective length of 23.5 cm the electrophoretic separation of the three inorganic anions could be achieved in <1 min, with detection limits of 0.05, 0.09 and 0.11 mg L^-1 for chloride, nitrate and sulfate, respectively. Also, the statistical t-test was applied to the results obtained for 82 rainwater samples that were collected and analyzed applying both the method developed in this study and the official APHA 4140 method where no statistical difference was noted within a 95% confidence level.

A data-driven approach for the detection of internal standard outliers in targeted LC-MS/MS assays

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Identifying internal standard outliers in clinical mass spectrometry assays is imperative.

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Current approaches for identifying outliers are arbitrary and do not account for assay drift.

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A robust modelling strategy allows laboratories to define their own acceptance criteria from their own data.

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This strategy is easily implemented and the code is freely available.

Heavy-labelled internal standard (IS) compounds are commonly used in liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays to control for stochastic and systematic variation. Identifying samples that suffer from unwanted variation is critically important in order to avoid factitiously inaccurate results. Current approaches for outlier detection typically employ arbitrary thresholds and ignore systematic drift. To improve this, we applied robust linear mixed-effects models (LMMs) to capture the within- and between-run variability in IS signal and generate data-driven acceptance ranges for routine use.

Data from in-house LC-MS/MS assays for 25-hydroxyvitamin D₃ and D₂ and prednisolone were retrospectively collected. The variation in the percentage deviation of the internal standard area from the mean of the calibrators was modelled through the use of robust LMMs. The fitted LMMs revealed significant positive drift in IS signal over the analytical runs for vitamin D, with slope coefficients of 0.118 (95% CI: 0.098, 0.138) and 0.192 (0.168, 0.215) for D₃ and D₂, respectively. In contrast, the models for prednisolone demonstrated a significant negative drift in IS signal, with a slope coefficient of −0.164 (−0.297, −0.036). Non-parametric, cluster bootstrap resampling enabled us to define acceptance ranges for use in future assays.

Here, we have described a computational approach to extensively characterise the variation in IS signal in routinely-performed LC-MS/MS assays. This approach facilitates a robust quality assessment of IS outliers in routine practice and thus has the potential to improve patient safety. Importantly, this approach is applicable to other MS assays where linear variation in IS signal is observed.

Determination of phosphite (HPO3-2) by a new IC/MS/MS method using an 18O-labeled HPO3-2 internal standard

A new method has been developed to determine trace amounts of phosphite (HPO₃^-2) in environmental samples using ion chromatography with electrospray tandem mass spectrometry (IC-ESI/MS/MS). The method includes the production and use of an ¹⁸O-labeled HPO₃^-2 internal standard (IS). This isotopically labeled IS significantly improved sensitivity and could account for matrix suppression. The method detection limit (MDL) was determined as 0.017 and 0.034 μg L^-1 of HPO₃^-2 (6.5 and 13 ng P L^-1) using a 500 and 25 μL injection loop, respectively. Precision (1-10%) and accuracy (recoveries = 96-106%) were established for a range of environmental samples using known (spiked) addition. The impact of ionic interferences was investigated by evaluating the response of the internal standard in the presence of common anions with respect to distilled deionized water. The most significant interference was due to nitrate (100 mg-NO₃^- L^-1) with a 99.99% reduction in IS intensity. The method was successfully applied to wastewater effluent, surface water, tap water, and soil samples. Relatively low concentrations <0.25 μg HPO₃^-2 L^-1 were measured in tap water, surface water and wastewater effluent, and ~1.6 μg kg^-1 HPO₃^-2 in soil samples, using both injection loops. Limited suppression was observed for all matrices. The largest IS peak area suppression (~98%) was observed in WW effluent with 500 μL injection loop; however, this method was able to quantify HPO₃^-2 with good recoveries and precision despite the mentioned suppression, supporting the ability of the proposed method to quantify HPO₃^-2 in different environmental matrices.

Preparation of racemic α-amino acid standards for accurate mass spectrometric analysis via racemization catalyzed by a hydrophobic pyridoxal derivative

Racemic α-amino acid standards for chiral metabolomics were prepared from l-α-amino acids using a hydrophobic pyridoxal derivative, namely 3-hydroxy-2-methyl-5-((octyloxy)methyl)isonicotinaldehyde (OPy), as the racemization catalyst. Among the 19 tested proteinogenic amino acids, 13 (including the generally unstable asparagine, glutamine, and tryptophan) underwent efficient racemization/epimerization under mildly basic conditions at room temperature, while solid-phase extraction allowed for effective and simple catalyst removal and amino acid recovery, obviating the need for chromatographic separation and recrystallization. Isotopically labeled racemic amino acids are commonly employed as internal standards for highly accurate mass spectrometric analysis. However, as isotopically labeled d-amino acids are often unavailable or highly expensive, the developed method was used to prepare racemic labeled amino acids, which were shown to enhance the repeatability and accuracy of d,l-amino acid quantitation in human urine by liquid chromatography-mass spectrometry (LC-MS). Given that our method should also be applicable to non-proteinogenic α-amino acids and the N-termini of peptides, the present study is expected to accelerate the development of LC-MS-based chiral metabolomics.

Quantitative SERS sensor based on self-assembled Au@Ag heterogeneous nanocuboids monolayer with high enhancement factor for practical quantitative detection

Accurate and rapid quantitative detection of pesticide and pollutant levels in the actual sample can aid in protecting food security, environmental security, and human health. A high Raman enhancement factor and good repeatability of the surface-enhanced Raman spectroscopy (SERS) substrates are favorable to quantitative analysis. Herein, a quantitative SERS sensor based on constructed self-assembled plasmonic Au@Ag heterogeneous nanocuboids (Au@Ag NCs) monolayer was developed. The sensor was used to quantitatively detect the trace pesticides extracted from pear surfaces and pollutants in fishpond water. Densely packed Au@Ag NCs fabricated into large-scale monolayer films were chemically functionalized using 4-methyl-thiobenzoic acid (4-MBA) at the organic/aqueous interface, in which plentiful nanogaps contribute to increase hotspots. Their sharp corners and edges make the sensor have high SERS performance through providing abundant "hot spots." The obtained optically SERS-based sensor with uniform liquid-state interfacial nanoparticle arrays appeared to have nice SERS performance and uniformity using crystal violet (CV) as a probe molecule. In particular, the proposed SERS sensor was applied for quantitative detection of thiabendazole (TBZ) extracted from pear surfaces and malachite green (MG) in fishpond water down to levels of 0.0105 nM and 0.87 nM for SERS assay respectively. As a result, our proposed SERS quantitative detection strategy is quite preferred to on-site analysis and supervision of contaminant in food samples.

Genome-wide association study identifies the virulence-associated marker in Streptococcus suis serotype 2

Streptococcus suis (S. suis) has been reported to be a highly invasive pathogen in swine, which causes severe infections like meningitis, arthritis and septicemia, and also a zoonotic agent for humans. Although many putative virulence factors (VFs) have been identified, the exact and wildly accepted virulence associated marker and pathogenesis mechanism of S. suis are still unclear. To establish connection of the genotypes with virulence phenotypes, we performed an "internal standard" method based on the zebrafish model to assess the virulence phenotypes of S. suis and did the genome-wide association study (GWAS) based on the genomes of 68 S. suis isolates. Through GWAS, a total number of 172 genes were identified. Among these genes, 143 of them distribute in virulent isolates. Further VFs interaction network analysis based on protein-protein interaction database found that 71 genes identified in this study could interact with known VFs and some of them even played an important role as the bridge between known VFs or formed important hub. In addition, 12 genes were found conserved in virulent isolates and 3 genes were conserved in avirulent isolates, 8 genes of the virulent conserved genes were belonging to a srtBCD pili cluster. Considering that sbp2', a member of the srtBCD pili cluster has been reported as a virulence-associated factor, we predict that sbp2' could be a fitness virulence-associated marker of virulent isolates. Taken together, our findings contribute to the insights in S. suis pathogenesis, enhance the knowledge of the genomic evolution of S. suis and provide several novel virulence-associated candidates.

An assumption-free quantitative polymerase chain reaction method with internal standard

In real-time quantitative polymerase chain reaction (PCR), the standard curve between threshold cycle and logarithm of template concentration is currently the gold standard for template quantification. The efficacy of this approach is limited by the necessary assumption that all samples are amplified with the same efficiency. To overcome this limitation, a new method has been proposed in this contribution for quantitative PCR with internal standard. Unlike existing methods based upon analysis of amplification profile position, the new method tries to determine the initial quantity of the target template in a sample from the fluorescence spectrum measured at a certain point during its PCR reaction. There is no unrealistic prerequisite (e.g., constant amplification efficiency) for the successful application of the new method. The performance of the new method was evaluated by the quantification of KRAS gene in HepG2 samples. Quantitative results with recovery rates in the range of 91.2-118% were achieved by the new method. It is reasonable to expect that the new method would have a place in real-time quantitative PCR, thanks to its features of no unrealistic prerequisite, sound theoretical basis, good performance, and implementation simplicity.

High performance liquid chromatographic assay of amlodipine, valsartan and hydrochlorothiazide simultaneously and its application to pharmaceuticals, urine and plasma analysis

A Simple, Specific, Precise, Accurate, Linear, Rugged, Robust High Performance Liquid Chromatographic method of analysis for simultaneous determination of assay of Amlodipine, Valsartan and Hydrochlorothiazide drugs in the pharmaceuticals tablet formulations using Pioglitazone as a common internal standard was developed and validated. The assay was accomplished using a mixture of acetonitrile & methanol in the volume ratio of 20:80 v/v (mobile phase B) and Ammonium acetate buffer (Mobile phase A) in gradient flow as mobile phase on an Hibar RP-18e, 250 × 4.6 mm, 5µ as chromatographic column at a flow rate of 1.300 mLmin-1, injection volume 10 µL and at a wavelength 235 nm with UV detector. Linearity of the analytical method was evaluated at a concentration range of 2.5-45.3 µg/ml for Amlodipine, 32.0-720.1 µg/ml for valsartan and 5.0-112.6 µg/ml for Hydrochlorothiazide respectively with Correlation coefficient (r) value more than 0.9997. The limit of detection (LOD) for Amlodipine, Valsartan and Hydrochlorothiazide was found to be 1.1 µg/ml, 8.0 µg/ml & 1.0 µg/ml respectively. Specificity, Method Precision, System Precision, Ruggedness, Robustness, Recovery, Stability of analytical solution, Filter paper selection study, Stress testing (Force Degradation) at various conditions were performed as per the ICH (Q2) recommendations. The chromatographic method may also be applied for simultaneous estimation of analytes in plasma and urine.

Quantitation of sex-specific serum N-glycome changes in expression level during mouse aging based on Bionic Glycome method

Studying the changes of serum N-glycome during mouse aging is beneficial to explore the molecular basis behind the alterations reported in human. However, such studies remainscarce and lack some information such as sialylation due to the method limitation. Here, we introduced Bionic Glycome method to quantify the serum N-glycome changes during C57BL/6 mouse aging (from the pubertal period to the old age stage). This technique enabled reliable and comprehensive quantitation of the expression level changes of more than 20 N-glycans in mouse serum at 12 time points in both genders for the first time, involving the analysis of sialic acid and its different linkages. The results demonstrated that the expression level of total glycans increased from middle age to old age. Interestingly, sex-specific N-glycome profiles and alterations were observed. Female mice showed higher level of serum fucosylation and lower level of serum afucosylation than male mice (fucosylation: p < 1.0E-6; afucosylation: p < 1.0E-6). Obviously, higher increase of serum fucosylation level was found in female mice than in male mice from middle age to old age. In addition, the opposite alterations of the afucosylated glycans with α2,3-linked sialic acid and those only with α2,6-linked sialic acid were observed at old age in male mice. These findings suggested that N-glycome could be a valuable target for investigating aging and possible contributors to aging.

A dataset for anthocyanin analysis in purple-pericarp sweetcorn kernels by LC-DAD-MS

This dataset refers to the accompanying article “Optimization of extraction procedure and development of LC-DAD-MS methodology for anthocyanin analysis in anthocyanin-pigmented corn kernels”, published in Food Chemistry [1]. Here, we present concentrations, profiles, MS² spectra of individual anthocyanins (including isomers of cyanidin-3-(6’’-malonylglucoside)) of purple-pericarp sweetcorn (PPS) kernels. Furthermore, an additional mass spectrum of an artefact-anthocyanin produced in acidified extraction solutions were reported. This data is further discussed in the accompanying research article [1]. Delphinidin-3-glucoside was used as an internal standard to compensate for individual anthocyanin losses during extraction with acidified solutions. The generated data could be used for anthocyanin identification and quantification in different anthocyanin-containing plant matrices.

Data on the optimisation of GC-MS/MS method for the simultaneous determination of compounds from food contact material

Food contact materials (FCM) made of plastic materials contain various additives, e.g. plasticisers, UV-stabilisers, preservatives, antioxidants, etc. These compounds can migrate from the material to the food and display adverse health effects in consumers. Inertness of FCM is established by migration testing with appropriate food simulants [1]. A GC-MS/MS method for the simultaneous determination of several different groups of additives to plastics has been developed to perform a migration testing and to determine these compounds in real samples, as described in the research publication "Development of a SPME-GC-MS/MS method for the determination of some contaminants from food contact material in beverages" [2]. Here, we present the data on the optimisation of GC-MS/MS parameters: GC column and temperature programme choice, MS/MS parameters optimisation, and choice of internal standard. Subsequently, SPME parameters were also optimised as described in [2].

Role of Jasmonate in Modulation of Mycorrhizae-Induced Resistance Against Fungal Pathogens

Symbiotic association of plants with arbuscular mycorrhizal (AM) fungi brings about changes in levels of the phytohormone jasmonate (JA) in root and shoot tissues of a plant. The enhanced JA levels not only play a role in controlling the extent of AM colonization but are also involved in the expression of mycorrhizal-induced resistance (MIR) against pathogens. We describe a method used to study the levels of a volatile jasmonate derivative, methyl jasmonate (MeJA), in tomato plants colonized by AM fungi and in response to subsequent attack by the foliar pathogen Alternaria alternata.

Preparation of uniformly labelled 13C- and 15N-plants using customised growth chambers

BACKGROUND

Stable isotopically labelled organisms have found wide application in life science research including plant physiology, plant stress and defense as well as metabolism related sciences. Therefore, the reproducible production of plant material enriched with stable isotopes such as ¹³C and ¹⁵N is of considerable interest. A high degree of enrichment (> 96 atom %) with a uniformly distributed isotope (global labelling) is accomplished by a continuous substrate supply during plant growth/cultivation. In the case of plants, ¹³C-labelling can be achieved by growth in ¹³CO_2(g) atmosphere while global ¹⁵N-labelling needs ¹⁵N- containing salts in the watering/nutrient solution. Here, we present a method for the preparation of ¹³C and ¹⁵N-labelled plants by the use of closed growth chambers and hydroponic nutrient supply. The method is exemplified with durum wheat.

RESULTS

In total, 330 g of globally ¹³C- and 295 g of ¹⁵N-labelled Triticum durum wheat was produced during 87 cultivation days. For this, a total of 3.88 mol of ¹³CO_2(g) and 58 mmol of ¹⁵N were consumed. The degree of enrichment was determined by LC-HRMS and ranged between 96 and 98 atom % for ¹³C and 95-99 atom % for ¹⁵N, respectively. Additionally, the isotopically labelled plant extracts were successfully used for metabolome-wide internal standardisation of native T.durum plants. Application of an isotope-assisted LC-HRMS workflow enabled the detection of 652 truly wheat-derived metabolites out of which 143 contain N.

CONCLUSION

A reproducible cultivation which makes use of climate chambers and hydroponics was successfully adapted to produce highly enriched, uniformly ¹³C- and ¹⁵N-labelled wheat. The obtained plant material is suitable to be used in all kinds of isotope-assisted research. The described technical equipment and protocol can easily be applied to other plants to produce ¹³C-enriched biological samples when the necessary specific adaptations e.g. temperature and light regime, as well as nutrient supply are considered. Additionally, the ¹⁵N-labelling method can also be carried out under regular glasshouse conditions without the need for customised atmosphere.

Applying an Internal Standard to Improve the Repeatability of In-electrospray H/D Exchange of Carbohydrate-Metal Adducts

In-electrospray (ESI) hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been used to characterize solvated carbohydrate structures. However, the rapid exchange rate of hydroxyls, as well as variations in source conditions and ambient humidity, alter the extent of forward and back exchange, resulting in poor repeatability when quantifying D-uptake on different days. Herein, we compare two internal standards, a peptide and derivatized carbohydrate, to improve the repeatability of in-ESI HDX of carbohydrate-metal adducts. Our results show that maltoheptaose, derivatized with Girard's T reagent, is a suitable internal standard for improving the repeatability of in-ESI HDX analyses of carbohydrates of varying size.

Identifying and Mitigating Errors in Screening for Organic Extractables and Leachables: Part 2-Errors of Inexact Identification and Inaccurate Quantitation

Patients can be exposed to leachables derived from pharmaceutical manufacturing systems, packages, and/or medical devices during a clinical therapy. These leachables can adversely decrease the therapy's effectiveness and/or adversely impact patient safety. Thus, extracts or drug products are chromatographically screened to discover, identify, and quantify organic extractables or leachables. Although screening methods have achieved a high degree of technical and practical sophistication, they are not without issues in terms of accomplishing these three functions. In this Part 2 of our three-part series, errors of inexact identification and inaccurate quantitation are addressed. An error of inexact identification occurs when a screening method fails to produce an analyte response that can be used to secure the analyte's identity. The error may be that the response contains insufficient information to interpret, in which case the analyte cannot be identified or that the interpretation of the response produces an incorrect identity. In either case, proper use of an internal extractables and leachables database can decrease the frequency of encountering unidentifiable analytes and increase the confidence that identities that are secured are correct. Cases of identification errors are provided, illustrating the use of multidimensional analysis to increase confidence in procured identities. An error of inaccurate quantitation occurs when an analyte's concentration is estimated by correlating the responses of the analyte and an internal standard and arises because of response differences between analytes and internal standards. The use of a database containing relative response factors or relative response functions to secure more accurate analyte quantities is discussed and demonstrated.

The use of dried matrix spot for determination of Pb and Ni in automotive gasoline by solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry

In this work a simple and practical method for the determination of Pb and Ni in automotive gasoline by solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry was investigated. In the proposed method, disks of filter paper were used to pre-concentrate and store Pb, Ni and other trace elements from automotive gasoline samples. For this, a volume of sample was deposited and dried out on a filter paper disk previously adapted into a polytetrafluoroethylene mold, and then the gasoline-embedded filter paper was either cut into small pieces or pulverised and introduced directly into the graphite furnace for trace element determination. Temperature program, use of chemical modifier, chromatographic effect and volume of sample were investigated. Calibration curves using organic and inorganic standards of the analytes as well as external and internal calibration methods were evaluated. Using optimised conditions, characteristic masses and limits of detection of 6 and 11 pg, and 0.5 and 2.1 μg L^-1 were found for Pb and Ni, respectively. The accuracy of the method was evaluated with spike-recovery tests and a certified reference material of wear lubricant oil. The spike-recovery tests were accomplished for 9 samples and the best results were obtained with the pulverised filter paper. A second method that employs a transversely heated filter atomiser was applied as a comparative one. The filter paper was shown to be a simple and inexpensive tool for storage and transportation of gasoline samples, and it allowed the pre-concentration of the analytes, since a larger volume of sample can be dried out on it.

Providing Bionic Glycome as internal standards by glycan reducing and isotope labeling for reliable and simple quantitation of N-glycome based on MALDI- MS

Accurate, simple and economical methods for quantifying N-glycans are continuously required for discovering disease biomarkers and quality control of biopharmaceuticals. Quantitative N-glycomics based on MS using exogenous isotopic labeling internal standards is promising as it is simple and accurate. However, it is largely hampered by the lack of available glycan internal standard libraries with good coverage of the natural glycan structural heterogeneity as well as broad dynamic mass and ion abundance range. To overcome this limitation, we developed a novel method, providing 'Bionic Glycome' as internal standards for glycan quantitation by MALDI-MS. Bionic Glycome was produced using N-glycome from pooled samples to be analyzed as substrate by one step of glycan reducing and isotope labeling (Glycan-RAIL). Each bionic glycan has 3 Da mass increment over its corresponding glycan analyte based on hemiacetals/alditols and H/D mass difference. In addition, Bionic Glycome has the same glycome composition and similar glycome profile in abundance with N-glycome to be analyzed from biological sample. Through the investigation of single glycan standard and complex glycans released from model glycoprotein and serum, the results demonstrate that the method has good quantitative accuracy and high reproducibility. Lastly, this method was successfully used for discovery of lung cancer specific glycan markers by comparing the serum glycans from each sample in lung cancer group (n = 16) and healthy controls (n = 16), indicating its potential in clinical applications.

An optimized assay for detecting Encephalitozoon intestinalis and Enterocytozoon bieneusi in dairy calf feces using polymerase chain reaction technology

The purpose of this study was to optimize primary and nested polymerase chain reaction (PCR) assays for detecting the microsporidia Encephalitozoon intestinalis and Enterocytozoon bieneusi in fecal samples from dairy calves. PCR for these microsporidia were compared to immunofluorescence assays (IFA) based on commercially available monoclonal antibodies specific for outer wall proteins of Enc. intestinalis or Ent. bieneusi. Fecal samples were collected from 15 dairy calves and processed by molecular sieving followed by salt floatation to recover Enc. intestinalis and Ent. bieneusi spores. An aliquot of the final supernatant was applied to glass slides for IFA testing; another aliquot was extracted for total DNA using a QIAamp Stool Mini-Kit for primary and nested Enc. intestinalis- and Ent. bieneusi-specific PCR analysis. Internal standards were generated for both Enc. intestinalis and Ent. bieneusi PCR assays to control for false negative reactions due to the presence of inhibitors commonly found in fecal samples. Using the commercial MicrosporIFA (Waterborne, Inc.) as the gold standard, the optimized Enc. intestinalis PCR method provided 85.7% sensitivity and 100% specificity with a kappa value = 0.865. Likewise, using the commercial BienusiGlo IFA (Waterborne, Inc.) as the gold standard, the optimized Ent. bieneusi PCR method provided 83.3% sensitivity and 100% specificity with a kappa value = 0.857. Sequencing of amplicons from both PCR assays confirmed the presence of Enc. intestinalis or Ent. bieneusi. In conclusion, our optimized assays for recovering and detecting Enc. intestinalis or Ent. bieneusi in feces from dairy calves provides a valuable alternative to traditional IFA methods that require expertise to identify extremely small microsporidia spores (~ 2.0 µm). Our assays also improve upon existing molecular detection techniques for these microsporidia by incorporating an internal standard to control for false negative reactions.

HPLC method for the assessment of tryptophan metabolism utilizing separate internal standard for each detector

The development of a validated method, applicable for the measurement of tryptophan (TRP) and serotonin (5-HT), and that of the neuroprotective branch of the kynurenine pathway from several different biological matrices, including mouse brain, is described. Following the spectral analysis of the metabolites, they were quantified with reversed-phase high-performance liquid chromatography (HPLC), using separate internal standards (ISs) for UV (3-nitro-L-tyrosine) and fluorescent (the newly utilized 4-hydroxyquinazoline-2-carboxylic acid) detectors. With regard to validation parameters, selectivity, linearity, limit of detection, limit of quantification, precision and recovery were determined. Although the linearity ranges were different for the assessed matrices, the correlation coefficient was >0.999 in each case. Furthermore, good intra- and inter-day precision values were obtained with coefficient of variation <5%, and bias <6.5% (except the 5-HT level in brain samples), respectively. The recoveries varied between 82.5% and 116%. The currently developed methods yield opportunities for the assessment of concentration changes in the TRP metabolism from a wide range of biological matrices, therefore they may well be utilized in future clinical and preclinical studies, especially in view that so many metabolites with the application of ISs have not been detected from mouse brain with such a simple HPLC method before.

Estimation of nuclear DNA content and its variation among Indian Tea accessions by flow cytometry

Nuclear DNA content and genome size variation among 36 Indian tea accessions were analyzed by flow cytometry. Initial standardization of protocols for isolation of nuclei, DNA staining and selection of an internal standard for tea accessions which have significantly high amount of phenolic secondary metabolites in their cytosol was carried out. Results obtained revealed that 2C DNA content of Indian tea is 7.46 pg which corresponds to 1C genome size of 3673 Mb. Inter accession variation in 2C DNA content was also observed among 35 diploid taxa ranging from 7.23 to 7.73 pg which was significant at 1% probability level. The 2C DNA content of triploid (UPASI 3) was observed to be 11.47 pg which is concurrent with the expected value. Results obtained showed that Assam and Cambod type tea accession have higher 2C DNA content of 7.73 pg whereas Assam Cambod hybrids and Assam China hybrids have reduction in DNA content with 2C amounts, 7.23 and 7.32 pg DNA respectively. The present study suggests that the species involved in origin of Indian tea must have differed in their genome sizes owing to significant inter accession variation in nuclear DNA content.

Application of 2D-DIGE and iTRAQ Workflows to Analyze CSF in Gliomas

Proteomics is an indispensable tool for disease biomarker discovery. It is widely used for the analysis of biological fluids such as cerebrospinal fluid (CSF), blood, and saliva, which further aids in our understanding of disease incidence and progression. CSF is often the biospecimen of choice in case of intracranial tumors, as rapid changes in the tumor microenvironment can be easily assessed due to its close proximity to the brain. On the contrary studies comprising of serum or plasma samples do not truly reflect the underlying molecular alterations due to the presence of protective blood-brain barrier. We have described in here the detailed workflows for two advanced proteomics techniques, namely, 2D-DIGE (two-dimensional difference in-gel electrophoresis) and iTRAQ (isobaric tag for relative and absolute quantitation), for CSF analysis. Both of these techniques are very sensitive and widely used for quantitative proteomics analysis.

Determination of squalene in edible oils by transmethylation and GC analysis

Squalene is a triterpenoid with medicinal, therapeutic and cosmetic applications. There is interest in identifying novel sources of squalene, creating a need for a rapid and accurate method of squalene determination. Here, we describe such an approach that involves first transmethylating the oil base containing squalene using a basic catalyst, followed by addition of internal standard and quantification by gas chromatography flame ionization detection (GCIFD).

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The method uses a single reference standard for quantification.

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Validation showed it to be both repeatable and accurate.

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It was successfully applied to nutraceutical and edible oils containing squalene.