A strategy for identifying species-specific peptide biomarkers in deer-hide gelatin using untargeted and targeted mass spectrometry approaches

Direct infusion-multiple reaction monitoring cubed (DI-MRM3) enables widely targeted bi-omics of Colla Corii Asini (Chinese name: Ejiao)

Food authenticity is extremely important and widely targeted bi-omics is a promising pipeline attributing to incorporating metabolomics and peptidomics. Colla Corii Asini (CCA, Ejiao) is one of the most popular tonic edible materials, with counterfeit and adulterated products being widespread. An attempt was devoted to develop a high-throughput and reliable DI-MRM3 program facilitating widely targeted bi-omics of CCA. Firstly, predictive MRM program captured metabolites and peptides in trypsin-digestive gelatins. After data alignment and structure annotation, primary parameters such as Q1 → Q3 → QLIT, CE, and EE were optimized for all 17 metabolites and 34 peptides by online ER-MS. Though a single run merely consumed 6.5 min, great selectivity was reached for each analyte. Statistical results showed that nine peptides contributed to distinguish CCA from other gelatins. After cross-validation with LC-MRM, DI-MRM3 was justified to be reproducible and high-throughput for widely targeted bi-omics of CCA, suggesting a meaningful tool for food authenticity.

Methods for detection and quantification of gelatin from different sources

Gelatin is a water-soluble protein obtained from the collagen of various animal origins (porcine, bovine, fish, donkey, horse, and deer hide) and has diverse applications in the food, pharmaceutical, and cosmetics industries. Porcine and bovine gelatins are extensively used in food and non-food products; however, their acceptance is limited due to religious prohibitions, whereas fish gelatin is accepted in all religions. In Southeast Asia, especially in China, gelatin obtained from donkey and deer skins is used in medicines. However, both sources suffer from adulteration (mixing different sources of gelatin) due to their limited availability and high cost. Unclear labeling and limited information about actual gelatin sources in gelatin-containing products cause serious concern among societies for halal and fraud authentication of gelatin sources. Therefore, authenticating gelatin sources in gelatin-based products is challenging due to close similarities between the composition differences and degradation of DNA and protein biomarkers in processed gelatin. Thus, different methods have been proposed to identify and quantify different gelatin sources in pharmaceutical and food products. To the best of our knowledge, this systematic and comprehensive review highlights different authentication techniques and their limitations in gelatin detection and quantification in various commercial products. This review also describes halal authentication and adulteration prevention strategies of various gelatin sources, mainly focussing on research gaps, challenges, and future directions in this research area.

Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics

Pheretima, also called "earthworms", is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines (CPMs) in Chinese Pharmacopoeia (2020 edition). However, its zoological origin is unclear, both in the herbal market and CPMs. In this study, a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms (restricted search, open search, and de novo) was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima, including Pheretima aspergillum (PA), Pheretima vulgaris (PV), and Metaphire magna (MM). We identified 10,477 natural peptides in the PA, 7,451 in PV, and 5,896 in MM samples. Five specific signature peptides were screened and then validated using synthetic peptides; these demonstrated robust specificity for the authentication of PA, PV, and MM. Finally, all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills, revealing the inconsistent Pheretima species used in these CPMs. In conclusion, our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines, especially non-model species with poorly annotated protein databases.

Identification and application of species-specific peptide biomarkers from soft-shelled turtles (Pelodiscus sinensis) using post-translational modification detection-based peptidomics analysis

The soft-shelled turtle is a commercially aquatic species in Asian countries, which serves as an important source of collagen with high nutritional and medicinal value, so it is of great significance to distinguish soft-shelled turtle derived collagen from others or adulterations. In this work, peptidomics analysis based on post-translational modification (PTM) assay was used to discover specific peptide biomarkers of soft-shelled turtle gelatin (STG). In total eight specific sequences and 74 peptides with different PTM types were screened out, and seven peptides with good signal responses and STG specificity were selected and validated as STG-specific peptide biomarkers. These peptide biomarkers could be used for distinguishing STG from other animal gelatins, and applied for ensuring the quality of collagens or gelatins from soft-shelled turtle with authenticity and traceability.

Discovery of species-specific peptide markers and development of quality-evaluation strategies for deer horn gelatin using liquid chromatography-tandem mass spectrometry and a label-free methodology

Deer horn gelatin (DHG) is a valuable nutritional dietary supplement. Due to the significant variation in the price of DHG from different sources, it is important to assess its quality and to clarify the species of its raw material. However, due to the similarity in appearance and physicochemical properties, as well as the destruction of genetic material during the manufacturing process, it is difficult to distinguish DHG from gelatin derived from other sources. Furthermore, current methods are unable to evaluate the overall quality of DHG. Using Nano LC-Orbitrap MS and data analysis software, DHG samples from five deer species were analyzed to identify peptide markers specific to alpha-2-HS-glycoprotein (AHSG) and collagen. The peptide markers were validated using HPLC-Triple Quadrupole MS, and strategies for assessing the quality of DHG were developed. Eighteen peptide markers were discovered, comprising peptides with differing specificities. Three strategies for the identification, characteristic mapping, and content determination of DHG were developed. These strategies can be used to assess the quality of deer gelatin.

Quantification of peptide components in cinobufacini injection and toad skin by ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry

Cinobufacini injection is commonly used in the clinical treatment of tumors and hepatitis B, but the quality is uneven. Currently, the main focus of its quality assessment is on steroids and alkaloids. Based on a previous study, we screened four peptides with high reproducibility, responsiveness, and specificity. This research was the first to develop an ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry approach for evaluating the quality of cinobufacini preparations from the peptide perspective. In this study, we have identified 230 peptides in cinobufacini injection by Q-Exactive mass spectrometry, which contains species-specific peptides. Then, we used ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry to establish a quantitative method for species-specific peptides and carried out method validation. The result revealed that four peptides were linear in a specific range, and had great reproducibility, accuracy, and stability. Eventually, we evaluated the quality of eight batches of cinobufacini injections and 26 batches of toad skins using the total content of target peptides as the criterion. The outcomes demonstrated that the quality of cinobufacini injection is generally stable and the toad skin from Shandong is of the best quality. In conclusion, the quantitative approach that focuses on peptides will offer innovative perspectives on assessing the quality of cinobufacini preparations.

A review on proteomic and genomic biomarkers for gelatin source authentication: Challenges and future outlook

Biomarkers are compounds that could be detected and used as indicators of normal and/or abnormal functioning of different biological systems, including animal tissues and food matrices. Gelatin products of animal origin, mainly bovine and porcine, are currently under scrutiny mainly due to the specific needs of some sectors of the population related to religious beliefs and their dietary prohibitions, as well as some potential health threats associated with these products. Thus, manufacturers are currently in need of a reliable, convenient, and easy procedure to discern and authenticate the origin of animal-based gelatins (bovine, porcine, chicken, or fish). This work aims to review current advances in the creation of reliable gelatin biomarkers for food authentication purposes based on proteomic and DNA biomarkers that could be applied in the food sector. Overall, the presence of specific proteins and peptides in gelatin can be chemically analysed (i.e., by chromatography, mass spectroscopy, electrophoresis, lateral flow devices, and enzyme-linked immunosorbent assay), and different polymerase chain reaction (PCR) methods have been applied for the detection of nucleic acid substances in gelatin. Altogether, despite the fact that numerous methods are currently being developed for the purpose of detecting gelatin biomarkers, their widespread application is highly dependent on the cost of the equipment and reagents as well as the ease of use of the various methods. Combining different methods and approaches targeting multiple biomarkers may be key for manufacturers to achieve reliable authentication of gelatin's origin.

Identification of Five Gelatins Based on Marker Peptides from Type I Collagen by Mass Spectrum in Multiple Reaction Monitoring Mode

In this study, a novel pseudo-targeted peptidomics strategy, integrating the transition list generated by an in-house software (Pep-MRMer) and the retention time transfer by high-abundance ion-based retention time calibration (HAI-RT-cal), was developed to screen marker peptides of gelatins from five closely related animal species, including porcine, bovine, horse, mule, and donkey. Five marker peptides were screened from the molecular phenotypic differences of type I collagen. Furthermore, a simple and robust 10 min multiple reaction monitoring (MRM) method was established and performed well in distinguishing different gelatins, particularly in discerning horse-hide gelatin (HHG) and mule-hide gelatin (MHG) from donkey-hide gelatin (DHG). The market investigation revealed the serious adulteration of DHG. Meantime, the pseudo-targeted peptidomics could be used to screen marker peptides of other gelatin foods.

Qualitative and Quantitative Analysis of Ejiao-Related Animal Gelatins through Peptide Markers Using LC-QTOF-MS/MS and Scheduled Multiple Reaction Monitoring (MRM) by LC-QQQ-MS/MS

Donkey-hide gelatin, also called Ejiao (colla corii asini), is commonly used as a food health supplement and valuable Chinese medicine. Its growing popular demand and short supply make it a target for fraud, and many other animal gelatins can be found as adulterants. Authentication remains a quality concern. Peptide markers were developed by searching the protein database. However, donkeys and horses share the same database, and there is no specific marker for donkeys. Here, solutions are sought following a database-independent strategy. The peptide profiles of authentic samples of different animal gelatins were compared using LC-QTOF-MS/MS. Fourteen specific markers, including four donkey-specific, one horse-specific, three cattle-specific, and six pig-specific peptides, were successfully found. As these donkey-specific peptides are not included in the current proteomics database, their sequences were determined by de novo sequencing. A quantitative LC-QQQ multiple reaction monitoring (MRM) method was further developed to achieve highly sensitive and selective analysis. The specificity and applicability of these markers were confirmed by testing multiple authentic samples and 110 batches of commercial Ejiao products, 57 of which were found to be unqualified. These results suggest that these markers are specific and accurate for authentication purposes.

Application of peptide biomarkers in life analysis based on liquid chromatography-mass spectrometry technology

Biomedicine is developing rapidly in the 21st century. Among them, the qualitative and quantitative analysis of peptide biomarkers is of considerable importance for the diagnosis and therapy of diseases and the quality evaluation of drugs and food. The identification and quantitative analysis of peptides have been going on for decades. Traditionally, immunoassays or biological assays are generally used to quantify peptides in biological matrices. However, the selectivity and sensitivity of these methods cannot meet the requirements of the application. The separation and analysis technique of liquid chromatography-mass spectrometry (LC-MS) supplies a reliable alternative. In contrast to immunoassays, LC-MS methods are capable of providing the analytical prowess necessary to satisfy the demands of peptide biomarker research in the life sciences arena. This review article provides a historical account of the in-roads made by LC-MS technology for the detection of peptide biomarkers in the past 10 years, with the focus on the qualification/quantification developments and their applications.

Peptidomics: A Review of Clinical Applications and Methodologies

Improvements in both liquid chromatography (LC) and mass spectrometry (MS) instrumentation have greatly enhanced proteomic and small molecule metabolomic analysis in recent years. Less focus has been on the improved capability to detect and quantify small bioactive peptides, even though the exact sequences of the peptide species produced can have important biological consequences. Endogenous bioactive peptide hormones, for example, are generated by the targeted and regulated cleavage of peptides from their prohormone sequence. This process may include organ specific variants, as proglucagon is converted to glucagon in the pancreas but glucagon-like peptide-1 (GLP-1) in the small intestine, with glucagon raising, whereas GLP-1, as an incretin, lowering blood glucose. Therefore, peptidomics workflows must preserve the structure of the processed peptide products to prevent the misidentification of ambiguous peptide species. The poor in vivo and in vitro stability of peptides in biological matrices is a major factor that needs to be considered when developing methods to study them. The bioinformatic analysis of peptidomics data sets requires the inclusion of specific post-translational modifications, which are critical for the function of many bioactive peptides. This review aims to discuss and contrast the various extraction, analytical, and bioinformatics approaches used for human peptidomics studies in a multitude of matrices.

Discovery of peptide biomarkers by label-free peptidomics for discrimination of horn gelatin and hide gelatin from Cervus nippon Temminck

Gelatin and gelatin-based derivatives have been attracting worldwide attention as health-food ingredients. Deer horn gelatin (DCG), a well-known and expensive gelatin food in Asia, has suffered adulterants by adding deer-hide gelatin (DHG) in it. However, robust and effective methods which could differentiate DCG from DHG are still unavailable. This study is committed to discover peptide biomarkers to distinguish DCG from DHG using label-free peptidomics by nanoLC-MS/MS. Multivariate statistical analysis combined with glycosylation sites analysis of peptides was applied to visualize the difference between DCG and DHG. As a result, four peptide biomarkers for distinguishing DCG and DHG were confirmed and validated by UPLC-MS/MS and MRM mode, which was also used to calculate adulteration percentage in commercial samples. The presented strategy may be also particularly helpful in the in-depth authentication of food gelatins from different tissues of the same species.

Simultaneous determination of eight tryptic peptides in musk using high-performance liquid chromatography coupled with tandem mass spectrometry

In comparison of herbal medicines, less attention has been paid onto animal medicines, partially attributing to the protein-enriched property. Particularly, it is still challenging to conduct quality evaluation for the animal medicines because of the lack of a fit-for-purpose analytical tool. Herein, an attempt was made to propose a workflow allowing the quality assessment of animal medicines by LC-MS/MS, and musk that is one of the most precious traditional Chinese medicines was employed as a representative case for utility illustration. After the extraction of protein from musk with a well-defined protocol, tryptic digestion was conducted to hydrolyze proteins into peptides, and the peptide-enriched sample was subjected to nanoLC-Orbitrap MS measurement. The tandem mass spectral dataset was retrieved in Human Swiss-Prot FASTA database, and the sequences together with the sources of 733 tryptic peptides, in total, were annotated. Because of the abundant distributions, eight peptides were chosen as the analytes for quantitative measurements, and their quantitative MS parameters, such as ion transitions and collision energies, were rapid optimized in an authentic compound-free manner using online energy-resolved MS (ER-MS). On the other side, the annotated peptides were structurally consolidated via synthesizing reference peptides. When the synthetic peptides were applied for parameter optimization with the authentic compound-dependent manner, the values were almost identical with those from online ER-MS measurements. After being validated with diverse assays, the developed method was applied for the simultaneous determination of eight peptides in 28 batches of musk samples, including captive (C1-C18) and wild ones (W1-W10). Significant differences took place for the content patterns of concerned tryptic peptides between the captive and wild musk samples. Trace distributions occurred for DVDAAYMNK in most batches. Captive samples were rich of QSLEASLAETEGR, TLLDIDNTR, and EVATNSELVQSGK, whereas wild samples were able to accumulate YLGYLEQLLR. Together, the present study provided a meaningful approach for the quality evaluation of musk, as well as other peptide-enriched animal medicines, even if the absences of authentic peptides.

Collagen derived species-specific peptides for distinguishing donkey-hide gelatin (Asini Corii Colla)

Objective

As an important food therapy product with traditional Chinese medicine (TCM) applications, donkey-hide gelatin (Asini Corii Colla, ACC) has been used for thousands of years. However, till now few effective strategy had been proposed to distinguish ACC from other animal hide gelatins, especially closely related horse- and mule-hide gelatins, which was an embarrassment of ACC quality control.

Methods

Combined mass spectrometry and bioinformatic methods have been applied to identify and verify two ACC-specific peptides (Pep-1 and Pep-2) capable of distinguishing ACC from other closely related animal gelatins with high selectivity.

Results

It confirmed that these two peptides could be not only used for distinguishing ACC from highly homologous horse-hide and mule-hide gelatins as well as other animal hide gelatins.

Conclusion

The present study provides a simple method for species-specific peptides discovery, which can be used for assessing the quality of animal gelatin products, and ensure they are authenticable and traceable.

Real-time authentication of animal species origin of leather products using rapid evaporative ionization mass spectrometry and chemometric analysis

Increasing accounts of fraud and persistent labeling problems have brought the authenticity of leather products into question. In this study, we developed an extremely simplified workflow for real-time, in situ, and unambiguous authentication of leather samples using rapid evaporative ionization mass spectrometry (REIMS) coupled with an electric soldering iron. Initially, authentic leather samples from cattle, sheep, pig, deer, ostrich, crocodile, and snake were used to create a chemometric model based on principal component analysis and linear discriminant analysis algorithms. The validated multivariate statistical model was then used to analyze and generate live classifications of commercial leather samples. In addition to REIMS analysis, the microstructures of leathers were characterized by scanning electron microscopy to provide complementary information. The current study is expected to provide a high-throughput tool with superior efficiency and accuracy for authenticating the identity of leathers and other consumer products of biogenic origin.

Identification of peptide biomarkers for authentication of Atlantic salmon and rainbow trout with untargeted and targeted proteomics approaches and quantitative detection of adulteration

Atlantic salmon is often adulterated or substituted by rainbow trout with much lower price and quality. However, it is extremely difficult to distinguish Atlantic salmon and rainbow trout due to their similar appearance and close relationship in species. In the present work, untargeted and targeted proteomics approaches were both implemented to identify species-specific peptide biomarkers of Atlantic salmon and rainbow trout. Potential peptide biomarkers were obtained through matching HRMS data with UniProt database, screened by BLAST and then verified with real samples. Five peptide biomarkers were identified each for Atlantic salmon and rainbow trout. MRM method was established for quantitative measurement of rainbow trout Adulteration in Atlantic salmon, showing high sensitivity and repeatability. The biomarker peptide GDPGPGGPQGEQGVVGPAGISGDK was used for quantification. The limit of the detection (LOD) of adulteration of rainbow trout is 0.19%, and the limit of quantitation (LOQ) is 0.62%. Furthermore, this method was successfully applied to analyze a number of Atlantic salmon and Rainbow trout samples from different regions and different batches, as well as commercially available processed products.

Assessment of carbonic anhydrase 3 as a marker for meat authenticity and performance of LC-MS/MS for pork content

In recent years, food fraud is a global issue that has raised wide public concern. Mass spectrometry techniques have a significant advantage of qualitatively and quantitatively analyzing food authenticity, especially for highly processed meat products. In this work, a simple and specific, rapid resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the determination of pork content in processed meat products according to internal standard (ISTD) method. To improve the efficiency of sample preparation, simplified bead-beating and enzymolysis process were investigated. In contrast with different heat-stable and specific porcine-peptides, EPITVSSDQMAK, GGPLTAAYR, HDPSLLPWTASYDPGSAK from Carbonic anhydrase 3 proved to have an excellent quantitative ability, thus obtaining good linear relationship and satisfactory recovery. This method was successfully applied to different types of meat products, thus demonstrating that complex mixtures of pork content can be accurately quantified.

Targeted Quantification of Peptides Using Miniature Mass Spectrometry

Proteomics by mass spectrometry (MS) allows for the identification of amino acid/peptide sequences in complex mixtures. Peptide analysis and quantitation enables screening of protein biomarkers and targeted protein biomarker analysis for clinical applications. Whereas miniature mass spectrometers have primarily demonstrated point-of-care analyses with simple procedures aiming at drugs and lipids, it would be interesting to explore their potential in analyzing proteins and peptides. In this work, we adapted a miniature MS instrument for peptide analysis. A mass range as wide as 100-2000 m/z was achieved for obtaining peptide spectra using this instrument with dual linear ion traps. MS² and MS³ can be performed to analyze a wide range of peptides. The parameters of pressure, electric potentials, and solution conditions were optimized to analyze peptides with molecular weights between 900 and 1800 Da. The amino acid sequences were identified using both beam-type and in-trap collision-induced dissociation, and the results were comparable to those obtained by a commercial quadrupole time-of-flight mass spectrometer. With product ion monitoring scan mode, peptide quantitation was performed with a limit of detection of 20 nM achieved for the Met peptide. The method developed has also been applied to the analysis of the trypsin-digested cell lysate of SKBR3 cells with a low expression level of the Met gene.