Absolute quantification of protein NP24 in tomato fruit by liquid chromatography/tandem mass spectrometry using stable isotope-labelled tryptic peptide standard

Research Progress in Isotope Labeling/Tags-Based Protein Quantification and Metrology Technologies

Advanced liquid chromatogram-mass spectrometry (LC-MS) and automated large-scale data processing have made MS-based quantitative analysis increasingly useful for research in fields such as biology, medicine, food safety, and beyond. This is because MS-based quantitative analysis can accurately and sensitively analyze thousands of proteins and peptides in a single experiment. However, the precision, coverage, complexity, and resilience of conventional quantification methods vary as a result of the modifications to the analytic environment and the physicochemical characteristics of analytes. Therefore, specially designed approaches are necessary for sample preparation. Dozens of methods have been developed and adapted for these needs based on stable isotopic labeling or isobaric tagging, each with distinct characteristics. In this review, we will summarize the leading strategies and techniques used thus far for MS-based protein quantification as well as analyze the advantages and shortcomings of different approaches. Additionally, we provide an overview of protein metrology development.

Simultaneous detection of glycinin and β-conglycinin in processed soybean products by high-performance liquid chromatography-tandem mass spectrometry with stable isotope-labeled standard peptides

Glycinin and β-conglycinin are the two main allergic proteins in soybean. Due to their complex structures and lack of protein standards, it is difficult to achieve quantitative determination of these proteins in soybeans. In this study, an HPLC-MS/MS method was developed for the simultaneous determination of five subunits of glycinin (G1, G2, G3, G4, and G5) and three subunits of β-conglycinin (α, α', and β) in processed soybean products based on 8 specific peptides and their stable isotope-labeled peptides. Here, each specific peptide was derived from one of the above 8 subunits. When soy protein was extracted and digested with trypsin, 8 specific peptides, and corresponding stable isotope-labeled peptides were analyzed by HPLC-MS/MS. The linear range for the specific peptides was between 3.2 and 1000 ng/mL (R2 > 0.9955). The recoveries of added peptides ranged from 83.4% to 117.8%, and the intra-day precisions (% CV) were below 17.4%. The limit of quantification of each subunit of glycinin and β-conglycinin in processed soybean products (in terms of protein amount) was between 15.1 and 156.1 g/g. This method was successfully applied to the analysis of 8 subunits of glycinin and β-conglycinin in 68 different processed soybean products, which provides technical support for processed product quality evaluation and monitoring soybean processing technology.

Proteomic identification and quantification of Clostridium perfringens enterotoxin using a stable isotope-labelled peptide via liquid chromatography-tandem mass spectrometry

PURPOSE

Detection of Clostridium perfringens enterotoxin (CPE) in human stool is critical evidence of food poisoning. However, processing patient-derived samples is difficult and very few methods exist to confirm the presence of CPE. In this study, a technique was developed using proteomic analysis to identify and quantify CPE in artificial gut fluid as an alternative.

METHODS

The standard CPE was spiked into artificial gut fluids, and effective methods were developed by employing both a stable isotope-labelled internal standard peptide and liquid chromatography-tandem mass spectrometry (LC-MS/MS).

RESULTS

Proteotypic peptide EILDLAAATER formed by tryptic digestion was selected for quantitation of CPE. The peptide was identified using product ion spectra. Although the nontoxic peptides originating from CPE showed very low detectability in extraction and tryptic digestion, they could be detected with sufficient sensitivity using the method we developed. Based on a spiked recovery test at two concentrations (50 and 200 µg/kg), the recovery values were 85 and 78%, respectively. The relative standard deviations of repeatability and within-laboratory reproducibility were less than 8 and 11%, respectively. These standard deviations satisfied the criteria of the Japanese validation guidelines for residues (MHLW 2010, Director Notice, Syoku-An No. 1224-1). The limit of quantification (LOQ) was estimated to be 50 µg/kg. The combination of the product ion spectra and relative ion ratio supported CPE identification at the LOQ level.

CONCLUSIONS

To the best of our knowledge, this is the first report of proteomic analysis of CPE using LC-MS/MS. The method would greatly help in assessing CPE reliably.

Quantification of lectin in soybeans and soy products by liquid chromatography-tandem mass spectrometry

Lectin is one of the major anti-nutritional factors in soybeans and inhibits digestion of dietary protein. Here, an absolute quantification method was developed to detect lectin using synthetic peptide 183TTSWDLANNK192 as reference standard and corresponding isotope labeled peptide TTSWDLANNK (Alanine-13C3,15N) as internal standard to normalize results. After the ground soybeans and soy products were defatted with n-hexane and extracted with extraction buffer, the crude protein extract was digested on filter membrane by trypsin. Further, the enzymatic hydrolysis peptides were quantified using liquid chromatography-tandem mass spectrometry. The synthetic reference peptide showed a detection limit of 0.27 ng/mL and a linear relationship in the range of 3.2-1000 ng/mL (r2 > 0.997). Correspondingly, the detect limit of lectin in soybean samples was 35.5 μg/g. The results showed that the recoveries of the lectin in spiked samples ranged from 80.9% to 108.7% with intra-day precisions (% CV) less than 9%. The method was successfully used to evaluate lectin levels in hundreds of soybean seeds from different varieties and soy products from different soybean processing techniques. Furthermore, the method may provide a potential application as a general method for the ultrasensitive detection of various protein anti-nutritional factors in food.

Analysis of A1-type and A2-type β-casein in Maiwa Yak and Pien-niu milk by HPLC-high-resolution MS and tandem MS

In this study, a peptide-based method employing ultra high performance liquid chromatography electrostatic field orbitrap high-resolution mass spectrometry and triple quadrupole mass spectrometry was developed for quantification of A1-type and A2-type β-casein in milk from Yak, cows, and their offspring of crosses, Pien-niu. The specific peptides of A1-type and A2-type β-casein were screened and confirmed by protein software after analysis of high-resolution mass spectrometry. The multiple reaction monitoring method was established based on the qualitative results, and isotope-label peptides were used as internal standards. The linear correlation coefficients of this method were >0.99. The relative standard deviations of repeatability test were 0.2-3.6%. The recovery rate ranged from 93.3 to 114.4% with relative standard deviations <6% at three different spiking levels. The method was applied to analyze 45 milk samples from different species. The results showed that β-casein in Yak and Pien-niu milk was about 30% higher than that in cow milk. Furthermore, the β-casein in the Yak milk only contains A2-type β-casein. A1-type and A2-type β-casein coexist in most samples of Pien-niu and cow milk, a few samples contain only one type of β-casein. These results provide further understanding in nutritional value of milk from Yak and Pien-niu.

Utility of the Leptospermum scoparium Compound Lepteridine as a Chemical Marker for Manuka Honey Authenticity

Manuka honey is a premium food product with unique antimicrobial bioactivity. Concerns with mislabeled manuka honey require robust assays to determine authenticity. Lepteridine is a Leptospermum-specific fluorescent molecule with potential as an authenticity marker. We describe a mass spectrometry-based assay to measure lepteridine based on an isotopically labeled lepteridine standard. Using this assay, lepteridine concentrations in manuka honey samples strongly correlated with concentrations quantitated by either high-performance liquid chromatography-ultraviolet (HPLC-UV) or fluorescence. A derived minimum lepteridine threshold concentration was compared with the New Zealand regulatory definition for manuka honey to determine "manuka honey" authenticity on a set of commercial samples. Both methods effectively distinguished manuka honey from non-manuka honeys. The regulatory definition excludes lepteridine but otherwise includes the quantification of multiple floral markers together with pollen analysis. Our findings suggest that the quantification of lepteridine alone or in combination with leptosperin could be implemented as an effective screening method to identify manuka honey, likely to achieve an outcome similar to the regulatory definition.

Molecular Characterization of the Thaumatin-like Protein PR-NP24 in Tomato Fruits

Pathogenesis-related proteins play significant roles in plant responses to pathogen infection and environmental stresses. PR-5 proteins are thaumatin-like proteins (TLPs) and can improve plant resistance to diseases. In this study, a protein named PR-NP24 belonging to the PR-5 family was found to be specifically expressed in tomato exocarp. Subsequently, PR-NP24 and orthologous TLPs were identified in partial Solanaceae species. The differential expression patterns of the PR-NP24 protein in the exocarp of tomato were further analyzed, which resulted in a better understanding of PR-NP24 regulation in plant responses to abiotic and biotic stresses. Accumulation of PR-NP24 induced by salt (NaCl) treatment could promote plant resistance against invasive fungal pathogens. This study concluded that the regulation of PR-NP24 in tomato exocarp could possibly be applied to improve the harvest management of tomato fruits as well as be of practical significance to control the allergenic potentials of the fruits of other plants.

Quantification of Gly m 5.0101 in Soybean and Soy Products by Liquid Chromatography-Tandem Mass Spectrometry

Gly m 5.0101, the alpha subunit of β-conglycinin, is one of the major allergens found in soybeans that has been identified as causing an allergic reaction. Here, we developed a quantification method of Gly m 5.0101 with multiple reaction monitoring using the synthetic peptide 194NPFLFGSNR202 as the external standard. Firstly, the ground soybean was defatted and extracted with a protein extraction buffer. Then the crude extract was on-filter digested by trypsin and analyzed by liquid chromatography-tandem mass spectrometry. The selected peptide exhibited a detection limit of 0.48 ng/mL and a linear relationship in a concentration range from 1.6 to 500 ng/mL (r² > 0.99). The developed method was successfully applied to quantify the Gly m 5.0101 level in dozens of soybean varieties from different sources and soybean products derived from different processing techniques. The developed method could be used to further analyze β-conglycinin in soybean seeds combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis.

Standardization and Regulation of Allergen Products in the European Union

Product-specific standardization is of prime importance to ensure persistent quality, safety, and efficacy of allergen products. The regulatory framework in the EU has induced great advancements in the field in the last years although national implementation still remains heterogeneous. Scores of methods for quantification of individual allergen molecules are developed each year and also the challenging characterization of chemically modified allergen products is progressing. However, despite the unquestionable increase in knowledge and the subsequent improvements in control of quality parameters of allergen products, an important aim has not been reached yet, namely cross-product comparability. Still, comparison of allergen product potency, either based on total allergenic activity or individual allergen molecule content, is not possible due to a lack of standard reference preparations in conjunction with validated standard methods. This review aims at presenting the most recent developments in product-specific standardization as well as activities to facilitate cross-product comparability in the EU.

Shotgun Proteomics of Tomato Fruits: Evaluation, Optimization and Validation of Sample Preparation Methods and Mass Spectrometric Parameters

An optimized protocol was developed for shotgun proteomics of tomato fruit, which is a recalcitrant tissue due to a high percentage of sugars and secondary metabolites. A number of protein extraction and fractionation techniques were examined for optimal protein extraction from tomato fruits followed by peptide separation on nanoLCMS. Of all evaluated extraction agents, buffer saturated phenol was the most efficient. In-gel digestion [SDS-PAGE followed by separation on LCMS (GeLCMS)] of phenol-extracted sample yielded a maximal number of proteins. For in-solution digested samples, fractionation by strong anion exchange chromatography (SAX) also gave similar high proteome coverage. For shotgun proteomic profiling, optimization of mass spectrometry parameters such as automatic gain control targets (5E+05 for MS, 1E+04 for MS/MS); ion injection times (500 ms for MS, 100 ms for MS/MS); resolution of 30,000; signal threshold of 500; top N-value of 20 and fragmentation by collision-induced dissociation yielded the highest number of proteins. Validation of the above protocol in two tomato cultivars demonstrated its reproducibility, consistency, and robustness with a CV of < 10%. The protocol facilitated the detection of five-fold higher number of proteins compared to published reports in tomato fruits. The protocol outlined would be useful for high-throughput proteome analysis from tomato fruits and can be applied to other recalcitrant tissues.