Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.

Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.

The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods.

Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and ß-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.

Qualitative and Quantitative Analysis of Three-Dimensional Fluorescence Spectra by Improved Parallel Factor Analysis with Internal Standard Sample Embedding.

The strategy of parallel factor analysis, combined with the internal standard method, has been increasingly applied to the qualitative and quantitative analysis of three-dimensional fluorescence spectra of unknown mixed fluorophores. Nevertheless, the disparity in the number of fluorophores included in the internal standard sample set and the number included in test samples may impact the qualitative and quantitative outcomes of parallel factor analysis. In this work, we systematically established the framework of the parallel factor analysis with internal standard sample embedding (ISSE-PARAFAC) strategy. We applied this framework to six datasets representing two scenarios and a real dataset and conducted a detailed discussion on the effects of the disparity between the number of fluorophores in the internal standard sample set and the number in the test set on both qualitative and quantitative results. Additionally, we introduced an enhancement to PARAFAC by aggregating fluorophores with similar emission wavelengths, corresponding to the peaks of emission loadings (spectra) obtained from PARAFAC, as a single fluorophore. This aggregation aimed to mitigate the strong correlation between similar fluorophores. The results imply that the presence of irrelevant fluorophores in the internal standard sample set, whether increased or decreased, does not significantly affect the qualitative and quantitative analysis of target fluorophores in the test set. Moreover, we demonstrated that the improved parallel factor analysis with internal standard sample embedding not only fully decomposes the uncorrelated mixed fluorophores for qualitative analysis but also allows the established linear concentration model for fluorescent components to predict the corresponding fluorophore concentration of test samples, enabling quantitative analysis at the ppm level (mg/L).

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.

Variability of internal standard method calibration factors estimated with a multifactorial Taguchi experiment in the analysis of alcoholic products by gas chromatography with flame ionization detection.

This study compares the variability of relative response factors (RRFs) using Taguchi's multifactorial analysis for two internal standard (IS) methods in gas chromatography (GC) for quality control of alcoholic products. Methods where either ethanol or pentan-1-ol was used as an IS were compared. For ten volatile substances prescribed by legislation, the RRFs of both methods were compared under 27 different experimental conditions. The influence of parameters (control factors) such as ethanol content in the matrix, analyte concentration, injected volume, injector temperature, split ratio, and flame ionization detector temperature was evaluated. The selected control factors had values at one of the three levels to cover the commonly used ranges of their settings in the measuring system and to characterize the majority of alcoholic products commonly analyzed in practice. The obtained results showed that the biggest differences in the variability of the results between the two methods were found for the most strictly controlled substances in alcoholic products, acetaldehyde, and methanol, where the application of ethanol as an IS provides clearly better results. For both methods, the way control factors affect the repeatability of GC measurements expressed in the form of relative deviation was also evaluated.

An Inhibitor-Monitorable Single-Tube Duplex Quantitative Real-Time PCR Assay for the Detection of 'Candidatus Liberibacter asiaticus'.

Huanglongbing (HLB) is a citrus infectious disease caused by 'Candidatus Liberibacter' spp. Recently, it has begun to spread rapidly worldwide, causing significant losses to the citrus industry. Early diagnosis of HLB relies on quantitative real-time PCR assays. However, the PCR inhibitors found in the nucleic acid extracted from plant materials pose challenges for PCR assays because they may result in false-negative results. Internal standard (IS) can be introduced to establish a single-tube duplex PCR for monitoring the influence of the PCR inhibitor, but it also brings the risk of false-negative results because the amplification of IS may compete with the target. To solve this problem, we proposed a mutation-enhanced single-tube duplex PCR (mSTD-PCR) containing IS with mutant-type primers. By introducing the 3'-terminal mutation in the primer of IS to weaken its amplification reaction and its inhibition of 'Candidatus Liberibacter asiaticus' (CLas) detection, the sensitivity and quantitative accuracy of CLas detection will not be affected by IS. In evaluating the sensitivity of CLas detection using simulation samples, the mSTD-PCR showed consistent sensitivity at 25 copies per test compared with the single-plex CLas assay. The detection result of 30 leaves and 30 root samples showed that the mSTD-PCR could recognize false-negative results caused by the PCR inhibitors and reduce workload by 48% compared with the single-plex CLas assay. Generally, the proposed mSTD-PCR provides a reliable, efficient, inhibitor-monitorable, quantitative screening method for accurately controlling HLB and a universal method for establishing a PCR assay for various pathogens.

[Determination of perchlorate and chlorate in drinks by ultra-performance liquid chromatography-tandem mass spectrometry].

OBJECTIVE: To establish a method for determination of perchlorate and chlorate in drinks by ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS) based on isotopic internal standard method. METHODS: The perchlorate and chlorate residue in liquid drinks were extracted with methanol, in solid drinks with acetic acid solution, then centrifuged. The supernatant was cleaned-up with PSA/C18 cleanup tube. The separation of perchlorate and chlorate was carried out on a Acquity CSH fluorophenyl column(100 mm×2.1mm, 1.7 µm) and the detection was performed with tandem mass spectrometry with internal standard method for quantification. RESULTS: The peak area ratio of perchlorate and chlorate had a good linear relationship with their mass concentration within their respective linear ranges, with correlation coefficients(r) greater than 0.999. The limits of detection of perchlorate and chlorate were 0.2and 1 µg/L respectively and the limits of quantification were 0.5 and 3 µg/L respectively. The mean recoveries of two compounds were from 84.0% to 105.5% with relative standard deviations from 4.2% to 17.0% and 82.7% to 112.1% with relative standard deviations from 5.5% to 18.4%(n=6), respectively. The perchlorates in 11 kinds of beverage samples were 0.53-4.12 µg/L, chlorates were 3.27-61.86 µg/L. CONCLUSION: This method is simple, sensitive, accurate and reliable, which is suitable for the determination of perchlorate and chlorate in drinks.

Improving hydrodynamic injection in capillary electrophoresis by using the integral of pressure.

A careful analysis of the typical devices and conditions used during hydrodynamic injection in capillary electrophoresis shows that the Hagen-Poiseuille model for the laminar flow is valid, even during the transitions of pressure. Therefore, the monitoring of pressure becomes a reliable approach to evaluate the effective injected volume, because the volume is proportional to the integral of pressure (IoP) over time. A piezoresistive sensor was used to monitor the air pressure at headspace of the sample vial. A set of 18 injections at 50 mbar and different times were used to evaluate the use of the normalization of the peak areas of the analytes by the IoP to compensate for imperfection during the injection. There was a significant decrease in relative standard deviation (RSD), and the proposed approach presented results similar to the use of internal standard. In addition, a microcontroller was used not only to monitor the pressure but also to command a peristaltic pump and a solenoid valve creating a system that dynamically controls the applied pressure and stops the injection when the desired value of IoP is reached. The system was used in a proof of concept in which different combinations of pressure and time were used: 10 mbar × 50 s, 25 mbar × 20 s, 50 mbar × 10 s, 125 mbar × 4 s, and 250 mbar × 2 s. Despite the constraints posed by the flowrates of the peristaltic pump and the solenoid valve, the microcontroller effectively conducted the injections across this extensive range of conditions, resulting in an IoP RSD of 2.7%.

Machine learning-assisted internal standard calibration label-free SERS strategy for colon cancer detection.

Liquid biopsies have significance for early colon cancer screening and improving patient survival. Recently, several researchers have applied surface-enhanced Raman spectroscopy (SERS) for the label-free and non-invasive detection of serum. Most of these studies performed the assay using a mixture of noble metal nanoparticles (NMNPs) with serum. However, SERS analysis of serum remains a challenge in terms of reproducibility and stability, as NMNPs tend to aggregate when mixed with serum, resulting in a non-uniform distribution of hot spots. Here, we report on the non-invasive identification of colon cancer (CC) using an internal standard (IS)-calibrated label-free serum SERS assay in combination with machine learning. Serum SERS spectra of 50 CC patients and 50 health volunteers have been obtained using silver nanoparticle (Ag NP) colloid and mercaptopropionic acid-modified Ag NPs (Ag NPs-MPA) as the SERS substrates. Decision tree (DT), random forest (RF), and principal component and linear discriminant analysis (PCA-LDA) algorithms were utilized to establish the diagnosis model for SERS spectra data classifying. The results show that the RF model provides a high diagnostic accuracy compared to PCA-LDA. Following calibration with IS molecules, high diagnostic accuracy of over 90% and 100% specificity can be achieved with DT, RF, and PCA-LDA algorithms to differentiate between cancer and normal groups. The results from this exploratory work demonstrate that serum SERS detection combined with multivariate statistical methods and IS calibration has great potential for the non-invasive and label-free detection of CC.

LC-MS accurate quantification of a tryptic peptide co-eluted with an isobaric interference by using in-source collisional purification.

Interferences from isobaric and isomeric compounds represent a common problem in liquid chromatography coupled to mass spectrometry (LC-MS). In this paper, in-source purification and chromatographic separation were combined with the aim of identifying isobaric contamination and quantifying accurately a compound despite the presence of an isobaric co-eluted interference. This is achieved by totally fragmenting in-source the precursor ions of the isobaric interference providing then LC-pseudo-MS2 capability, which allows an accurate quantification without the need for optimizing the chromatographic conditions to separate the co-eluted interference. To illustrate this concept, mixtures of tryptic and non-tryptic peptides were used. The ratio of peak areas of the tryptic peptide and its isotopically labelled internal standard was used not only for quantification with an internal standard calibration curve but also to know (1) if an isobaric interference co-eluted with the tryptic peptide; and (2) what is the minimum cone voltage necessary to ensure the complete removal of isobaric interference. This strategy was applied to quantify the tryptic peptide of two standards with known concentrations and, intentionally contaminated with the isobaric interference. The confidence intervals of the concentrations calculated with the internal standard calibration curve were 8.0 ± 0.5 µM (prepared at 8.0 µM) and 15.7 ± 0.5 µM (prepared at 16.1 µM) that confirm the tryptic peptide can be correctly quantified by in-source purification without the need for improving the chromatographic separation from its isobaric interference.

Quantification of cefaclor in human plasma using SIL-IS LC-ESI-MS/MS for pharmacokinetics study in healthy Chinese volunteers.

A steady, high-efficiency, and precise liquid chromatography-electrospray ionization-tandem mass spectrometry method was established and validated using cefaclor-d5 as the stable isotope-labeled internal standard for quantification of cefaclor in human plasma. One-step protein precipitation was applied to extract human plasma samples using methanol as precipitant. An Ultimate XB C18 column (2.1 × 50.0 mm, 5.0 µm) was used to achieve chromatographic separation. Mobile phases of gradient elution were an aqueous solution containing 0.1% formic acid (mobile phase A) and an acetonitrile solution containing 0.1% formic acid (mobile phase B). Electrospray ionization in positive-ion mode was applied to detect under multiple reaction monitoring mode. Target fragment ion pairs of cefaclor and stable isotope-labeled internal standard, respectively, were m/z 368.2 → 191.1 and m/z 373.2 → 196.1. Linear range of this method was between 20.0 and 10,000.0 ng/ml, with coefficient of determination (R2 ) >0.9900. Seven concentrations of quality control samples were used: 20.0 ng/ml (lower limit of quantitation), 60.0 ng/ml (low quality control), 650 ng/ml (middle quality control), 5000 ng/ml (arithmetic average middle quality control [AMQC]), 7500 ng/ml (high quality control), 10,000 ng/ml (upper limit of quantification), and 40,000 ng/ml (dilution quality control [DQC]). The method was validated for selectivity, lower limit of quantitation, linearity, accuracy, precision, recovery, matrix effect, dilution reliability, stability, carryover, and incurred sample reanalysis. This stable isotope-labeled internal standard liquid chromatography-electrospray ionization-tandem mass spectrometry approach has been successfully applied to study the pharmacokinetics of cefaclor dry suspension among healthy Chinese volunteers.

Quantification of Oligonucleotides Using Tandem Mass Spectrometry with Isobaric Internal Standards.

In recent years, oligonucleotides have become more important in research, drug approvals and medical therapies. Due to this growing interest in pharmaceutical applications, it is essential to develop reliable analytical methods for this substance class. In this work, we present a quantification method using liquid chromatography coupled with tandem mass spectrometry by applying an isobaric oligonucleotide standard. In addition to a proof of principle, we perform a method qualification to assess its readiness for validation according to ICH Q2 guidelines. In addition to good linearity, sensitivity, accuracy and recovery, the method showed no significant matrix effects. Furthermore, we demonstrated the application of the method by applying the quantification in a biological matrix, as well as an exemplary degradation of an oligonucleotide in bovine plasma.

Determination of Response Factors for Analytes Detected during Migration Studies, Strategy and Internal Standard Selection for Risk Minimization.

Migration studies are one of the few domains of pharmaceutical analysis employing wide-scope screening methodologies. The studies involve the detection of contaminants within pharmaceutical products that arise from the interaction between the formulation and materials. Requiring both qualitative and quantitative data, the studies are conducted using Liquid Chromatography or Gas Chromatography coupled to a mass spectrometer (LC-MS and GC-MS). While mass spectrometry allows wide-scope analyte detection and identification at the very low Analytical Evaluation Threshold (AET) levels used in these studies, MS detectors are far from "universal response" detectors. Regulation brings the application of uncertainty factors into the picture to limit the risk of potential analytes detected escaping report and further evaluation; however, whether the application of a default value can cover any or all relevant applications is still debatable. The current study evaluated the response of species usually detected in migration studies, generating a suitable representative sample, analyzing said species, and creating a strategy and evaluation mechanism for acceptable classification of the detected species. Incorporating novel methodologies, i.e., Design of Experiments (DoE) for Design Space generation, the LC-MS-based methodology is also evaluated for its robustness in changes performed.

Quantification and toxicokinetics of paraquat in mouse plasma and lung tissues by internal standard surface-enhanced Raman spectroscopy.

Paraquat is a quaternary ammonium herbicide with an excellent herbicidal effect but is highly toxic to human and animals. Although prohibited by many countries, paraquat intoxication occurred occasionally and caused severe consequences. Rapid and accurate determination of paraquat concentration in intoxication samples is urgently needed in the clinic to promptly evaluate the prognosis of poisoning patients. Here we report an internal standard surface-enhanced Raman spectroscopy (IS-SERS) quantification method on paraquat in mouse plasma and lung tissues for the first time. One measurement per sample was fulfilled within 10 s via this IS-SERS method. Paraquat had good linearity in the range of 1 ~ 500 µg/L (plasma sample) and 1 ~ 100 µg/g (lung sample), with the LOD and LOQ of 0.5 µg/L and 0.1 µg/g (plasma sample), and 5 µg/L and 1 µg/g (lung sample), respectively. This IS-SERS method was validated according to the international guidelines and applied to a quantitative determination and the toxicokinetics on paraquat in mouse plasma and lung tissues. The results indicated that paraquat had a fast absorption rate and a slow elimination rate in mouse plasma and lung tissues. Paraquat was prone to accumulate in target organs after entering the blood. It also proved its good practical applicability in one clinical intoxication sample. Meanwhile, we unveiled an underestimation of free paraquat amount towards common biological sample pretreatment, a certain amount of paraquat bound to components with molecular weight less than 30 kDa in the plasma; we hope it could provide some interesting information for possible clinic treatment.

Trace determination of imidacloprid and its major metabolites in wheat-soil system.

Trace analysis method is a reliable basis for studying the translocation and metabolism of imidacloprid used as an insecticide in wheat, and it clarifies whether biologically active metabolites including residual imidacloprid, have long-lasting insecticidal potency against wheat aphids under seed treatment during the entire growth period. In this study, a highly sensitive analytical method was established to determine the residues of imidacloprid and its six metabolites (5-hydroxy imidacloprid, imidacloprid olefin, imidacloprid guanidine, imidacloprid urea, 6-chloronicotinic acid, and imidacloprid nitrosimine) in wheat-soil systems, such as in wheat leaves, wheat ears, wheat grains, roots, and soil. All the compounds were extracted using an ACN:water (8:2, v/v) mixture and purified by dispersive solid-phase extraction. The average recoveries ranged from 74.4% to 109.5% for all matrices, with intra- and inter-day variations of less than 14.9%. The limit of quantitation was in the range of 0.001-0.005 mg/kg. The method is demonstrated to be sensitive and accurate for monitoring imidacloprid and its metabolites at trace levels during the entire growth period under field conditions.

Development, validation, and clinical application of a rapid UPLC-MS/MS method for detection of colchicine in human whole blood and urine.

A rapid, simple, and economical method has been developed to determine colchicine in both human whole blood and urine using UPLC-MS/MS. Colchicine and isotope-labeled internal standard were extracted from the matrix by liquid-liquid extraction with saturated borax and ethyl acetate, and separated by a reversed-phase chromatography C18 column. Gradient elution was carried out using acetonitrile and water spiked with 0.01% formic acid. Multiple reaction monitoring was performed at positive ion mode. The quantitative transitions were m/z 400.27 → 310.28 for colchicine and m/z 406.16 → 313.18 for colchicine-D6. The method has good linearity in the range of 0.5-200 ng/mL for blood and 2-2000 ng/mL for urine. The sensitivity, accuracy, and matrix effect were all in line with the guidelines of Food and Drug Administration and European Medicines Agency. The extraction recovery was above 63.94%. The samples were stable under various storage conditions. Six deuterium-substituted isotopic internal standard was used to demonstrate a different mode of colchicine cleavage from the existing literature. This method has been successfully used in the diagnosis of patients with colchicine poisoning. Blood is recommended as the optimal sample compared with urine.

Establishment and validation of an SIL-IS LC-MS/MS method for the determination of ibuprofen in human plasma and its pharmacokinetic study.

In this work, we developed and validated a highly sensitive, rapid and stable LC-MS/MS method for the determination of ibuprofen in human plasma with ibuprofen-d3 as a stable isotopically labeled internal standard (SIL-IS). Human plasma samples were prepared by one-step protein precipitation. The chromatographic separation was achieved on a Poroshell 120 EC-C18 (2.1 × 50 mm, 2.7 µm). Aqueous solution (containing 0.05% acetic acid and 5 mm NH4 Ac) and methanol were selected as the mobile phase with gradient elution. An electrospray ionization source was applied and operated in negative ion mode. Multiple reaction monitoring mode was used for quantification using target fragment ions m/z 205.0 → 161.1 for ibuprofen and m/z 208.0 → 164.0 for SIL-IS, respectively. This method exhibited a linear range of 0.05-36 µg/ml for ibuprofen with correlation coefficient >0.99. Mean recoveries of ibuprofen in human plasma ranged from 78.4 to 80.9%. The RSD of intra- and inter-day precision were both < 5%. The accuracy was between 88.2 and 103.67%. The matrix effect was negligible in human plasma, including lipidemia and hemolytic plasma. A simple, efficient and accurate LC-MS/MS method was successfully established and applied to a pharmacokinetic study in healthy Chinese volunteers after a single oral administration of ibuprofen granules.

[Simultaneous determination of glucosinolates and flavonoids in leaves of Moringa oleifera by quantitative analysis of multi-components by single-marker (QAMS)].

To establish a method for simultaneously determining the content of four glucosinolates and five flavonoids in leaves of Moringa oleifera via quantitative analysis of multi-components by single-marker(QAMS) and verify the feasibility and applicability of the established method. The glucosinolates and flavonoids were analyzed via Waters Acquity UPLC HSS T_3 column(2.1 mm × 100 mm, 1.8 µm). The gradient elution was carried out with the mobile phase composed of 0.1% formic acid-acetonitrile and 0.3% formic acid at the flow rate of 0.4 mL·min~(-1) and the column temperature of 40 ℃. The wavelengths for the detection of glucosinolates and flavonoids were 225 nm and 260 nm, respectively. With 4-O-(α-L-rhamnoyloxy)-benzyl glucosinolate and vecenin-2 as internal reference substances, the relative correction factors of four glucosinolates and five flavonoids were respectively calculated for determining the content of the 9 ingredients in leaves of M. oleifera. To verify the accuracy and feasibility of QAMS, we used internal standard method(ISM) and external standard method(ESM) to determine the content of glucosinolates and flavonoids, respectively. The t-test results showed that there was no significant difference in the content of glucosinolates obtained by ISM and QAMS methods or in the content of flavonoids obtained by ESM and QAMS methods. The content of glucosinolates and flavonoids varied among M. oleifera of different varieties and from different producing areas. The total glucosinolates and total flavonoids had the highest content in the Indian variety while the lowest content in the variety ■Honghe No. 1'. The established QAMS method is rapid, simple and accurate and can be used for simultaneous determination of glucosinolates and flavonoids in the leaves of M. oleifera. This study provides experimental data for the quality control and utilization of M. oleifera leaves.

An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community.

Precise multiplexed quantification of proteins in biological samples can be achieved by targeted proteomics using multiple or parallel reaction monitoring (MRM/PRM). Combined with internal standards, the method achieves very good repeatability and reproducibility enabling excellent protein quantification and allowing longitudinal and cohort studies. A laborious part of performing such experiments lies in the preparation steps dedicated to the development and validation of individual protein assays. Several public repositories host information on targeted proteomics assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker, with all offering varying levels of details. We introduced MRMAssayDB in 2018 as an integrated resource for targeted proteomics assays. The Web-based application maps and links the assays from the repositories, includes comprehensive up-to-date protein and sequence annotations, and provides multiple visualization options on the peptide and protein level. We have extended MRMAssayDB with more assays and extensive annotations. Currently it contains >828 000 assays covering >51 000 proteins from 94 organisms, of which >17 000 proteins are present in >2400 biological pathways, and >48 000 mapping to >21 000 Gene Ontology terms. This is an increase of about four times the number of assays since introduction. We have expanded annotations of interaction, biological pathways, and disease associations. A newly added visualization module for coupled molecular structural annotation browsing allows the user to interactively examine peptide sequence and any known PTMs and disease mutations, and map all to available protein 3D structures. Because of its integrative approach, MRMAssayDB enables a holistic view of suitable proteotypic peptides and commonly used transitions in empirical data. Availability: http://mrmassaydb.proteincentre.com.

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.