Chemical Labeling Research Articles

A Highly Efficient Click Linker for Enrichment of Alkyne‐Tagged Proteins in Living Cells

Alkyne tags have been widely used for the enrichment of labeled proteins to enable their profiling at a proteome‐wide scale by mass spectrometry. The key component in the enrichment process is an azido‐terminated cleavable linker for capturing the labeled proteins/peptides via click reaction. Herein, we report a new efficient click linker (APA biotin) featuring an acid‐cleavable acetal linkage end‐caped with a highly reactive picolyl azido head and a biotin handle for anchoring onto streptavidin‐coated supports. Using an amine‐reactive probe to profile the proteome structural changes in living S. cerevisiae cells within 5 minutes of heat shock, we demonstrated that the linker allowed identification of >9400 labeled sites, among which 457‐1656 with significantly altered reactivity upon heat shock. This study represented the first chemical labeling mass spectrometry (CL‐MS)‐based profiling of proteome structural changes in living cells in response to external stimuli. Data are available via ProteomeXchange with identifier PXD051279.

ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs

Differences in gene-expression profiles between individual cells can give rise to distinct cell fate decisions. Yet how localisation on a micropattern impacts initial changes in mRNA, protein, and phosphoprotein abundance remains unclear. To identify the effect of cellular position on gene expression, we developed a scalable antibody and mRNA targeting sequential fluorescence in situ hybridisation (ARTseq-FISH) method capable of simultaneously profiling mRNAs, proteins, and phosphoproteins in single cells. We studied 67 (phospho-)protein and mRNA targets in individual mouse embryonic stem cells (mESCs) cultured on circular micropatterns. ARTseq-FISH reveals relative changes in both abundance and localisation of mRNAs and (phospho-)proteins during the first 48 hours of exit from pluripotency. We confirm these changes by conventional immunofluorescence and time-lapse microscopy. Chemical labelling, immunofluorescence, and single-cell time-lapse microscopy further show that cells closer to the edge of the micropattern exhibit increased proliferation compared to cells at the centre. Together these data suggest that while gene expression is still highly heterogeneous position-dependent differences in mRNA and protein levels emerge as early as 12 hours after LIF withdrawal.

Hybrid Small-Molecule/Protein Fluorescent Probes.

Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.

Salivary metabolomic identification of biomarker candidates for oral melanoma and oral squamous cell carcinoma in dogs.

Oral melanoma (OM) and oral squamous cell carcinoma (OSCC) are frequently diagnosed in dogs, presenting a challenge in distinguishing them from benign oral tumors (BN). Salivary metabolomic biomarkers offer a practical solution because of saliva's direct contact with tumors and the noninvasive nature of collection. Assess the diversity and abundance of the salivary metabolome in dogs with BN, OM, and OSCC using amine/phenol submetabolome analysis and high-performance chemical isotope labeling liquid chromatography-mass spectrometry (CIL LC-MS). Study included 11 BN, 24 OM, 10 OSCC, and 20 healthy control dogs. Case-control cross-sectional study was conducted to assess salivary submetabolic profiles in dogs with BN, OM, and OSCC and healthy dogs. Samples were labeled with 12C-dansyl chloride and analyzed using CIL LC-MS targeted to amine- and phenol-containing metabolites for amine/phenol submetabolome analysis. Distinct clusters and significant differences in metabolite concentrations were observed among the oral cancer, BN, and control groups. A total of 154 and 66 metabolites showed significantly altered concentrations, particularly in OM and OSCC, respectively, when compared with BN (Padj < .05). Potential metabolic biomarkers were identified for each cancer, including decreased concentrations of seryl-arginine and sarcosine in OSCC. Moreover, high-confidence putative metabolites were identified, including an increase in tryptophyl-threonine and a decrease in 1,2-dihydroxynapthalene-6-sulfonic acid and hydroxyprolyl-hydroxyproline for OM. We identified high coverage of the amine/phenol submetabolome, including seryl-arginine, and sarcosine, in OSCC. Our findings emphasize the potential of these biomarkers for distinguishing between oral OSCC and BN in dogs.

Abstract PO4-05-05: Immune Activation Signatures for predicting CDKi primary response in advanced breast cancer patients

Abstract Background Cyclin Dependent Kinase inhibitors (CDKi’s) in combination with Endocrine Therapy (ET) have changed the first line management of patients with the most common subtype (HR+, HER2-) of metastatic breast cancer (MBC), improving progression-free survival (PFS) and overall survival. However, in approved indications for advanced breast cancer, approximately 20% of patients have been observed to have no response to CDKi’s and ET, and to progress after starting these therapies. Unlike other targeted therapeutics, there is no companion diagnostic or other clinically reliable biomarker for clinical decision support to indicate which patients will and will not benefit from CDKi therapy. Methods We have developed a novel platform that measures the Immune Activation Signature of patient plasma samples. Via simple measurements of the total concentration of protein-incorporated amino acid residues within patient plasma samples, the platform is designed to reveal changes in the proportion of immunoglobulins and albumin, and class-switching among immunoglobulins. For that purpose, we use Bioorthogonal chemical labelling reactions to label the protein-incorporated amino acids residues within the plasma. We measured the plasma samples of N=30 HR+, HER2- MBC patients, median age 54 years old, who were baseline naïve for CDKi’s treatment (16 on palbociclib, 11 on ribociclib, and 3 on abemaciclib) and ET. Eighteen patients had metastatic visceral disease and 12 patients had bone-only MBC. All patients were prospectively followed, and response assessed according to RECIST criteria on a CT scan every 3-months. Results Non-responding patients developed objective progressive disease during the first 6 months after starting CDKis and ET. In this cohort, 4 patients (13%) were classified as non-responders. The median PFS in non-responding patients was 4.5 months (4.03-5.02) and the median PFS in the cohort of responding patients was 16.6 months (6.8 – 40.9). The Immune Activation Signatures of the Responding and Non-Responding patients are shown in table 1. We analyzed the results with classical statistics and machine learning. A multivariate analysis of variance (MANOVA) test of the null hypothesis that the Immune Activation Signatures of Non-Responders and Responders are the same gave p = 0.00388. We analyzed the measured Immune Activation Signatures using a supervised machine learning classifier and observed in a held-back validation set correct prediction of 100% of non-responding patients and 95% accurate predictions overall. Conclusions According to these results, this platform may provide a clinically helpful biomarker for clinical decision support in the advanced or aggressive breast cancer context (patients with visceral metastasis bordering on visceral crisis), or for patient stratification in new indications. Table. Immune Activation Signature measurements (mean values in Clinical Outcome) Citation Format: Luis Costa, Cong Tang, Emma Yates, Qi Shi, Wesley Sukdao, Patricia Corredeira, Gonçalo Costa, Helena Pais, Catarina Abreu, Leonor Ribeiro, Rita Teixeira de Sousa, Sofia Torres, André Mansinho, Sandra Casimiro, Ana Cavaco, Patricia Alves, Angela Rodrigues, Lisiana Szeneszi, Gonçalo Bernardes. Immune Activation Signatures for predicting CDKi primary response in advanced breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-05-05.

Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics

Aphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC–MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.

Unraveling the enigma: housekeeping gene Ugt1a7c as a universal biomarker for microglia.

Microglia, brain resident macrophages, play multiple roles in maintaining homeostasis, including immunity, surveillance, and protecting the central nervous system through their distinct activation processes. Identifying all types of microglia-driven populations is crucial due to the presence of various phenotypes that differ based on developmental stages or activation states. During embryonic development, the E8.5 yolk sac contains erythromyeloid progenitors that go through different growth phases, eventually resulting in the formation of microglia. In addition, microglia are present in neurological diseases as a diverse population. So far, no individual biomarker for microglia has been discovered that can accurately identify and monitor their development and attributes. Here, we highlight the newly defined biomarker of mouse microglia, UGT1A7C, which exhibits superior stability in expression during microglia development and activation compared to other known microglia biomarkers. The UGT1A7C sensing chemical probe labels all microglia in the 3xTG AD mouse model. The expression of Ugt1a7c is stable during development, with only a 4-fold variation, while other microglia biomarkers, such as Csf1r and Cx3cr1, exhibit at least a 10-fold difference. The UGT1A7C expression remains constant throughout its lifespan. In addition, the expression and activity of UGT1A7C are the same in response to different types of inflammatory activators' treatment in vitro. We propose employing UGT1A7C as the representative biomarker for microglia, irrespective of their developmental state, age, or activation status. Using UGT1A7C can reduce the requirement for using multiple biomarkers, enhance the precision of microglia analysis, and even be utilized as a standard for gene/protein expression.

Efficient Supervised Pretraining of Swin-Transformer for Virtual Staining of Microscopy Images.

Fluorescence staining is an important technique in life science for labeling cellular constituents. However, it also suffers from being time-consuming, having difficulty in simultaneous labeling, etc. Thus, virtual staining, which does not rely on chemical labeling, has been introduced. Recently, deep learning models such as transformers have been applied to virtual staining tasks. However, their performance relies on large-scale pretraining, hindering their development in the field. To reduce the reliance on large amounts of computation and data, we construct a Swin-transformer model and propose an efficient supervised pretraining method based on the masked autoencoder (MAE). Specifically, we adopt downsampling and grid sampling to mask 75% of pixels and reduce the number of tokens. The pretraining time of our method is only 1/16 compared with the original MAE. We also design a supervised proxy task to predict stained images with multiple styles instead of masked pixels. Additionally, most virtual staining approaches are based on private datasets and evaluated by different metrics, making a fair comparison difficult. Therefore, we develop a standard benchmark based on three public datasets and build a baseline for the convenience of future researchers. We conduct extensive experiments on three benchmark datasets, and the experimental results show the proposed method achieves the best performance both quantitatively and qualitatively. In addition, ablation studies are conducted, and experimental results illustrate the effectiveness of the proposed pretraining method. The benchmark and code are available at https://github.com/birkhoffkiki/CAS-Transformer.

Assessing Therapy and Rehabilitation Comprehension of Chemical Labelling and Forming Chemical Safety Competence Specialists

Introduction. Considering the higher risk of man-made chemical disasters due to military operations, the demand for the training of qualified therapists and rehabilitators is increasing. Future healthcare professionals should be competent in chemical safety and fully possess information on the designation and classification of hazardous substances and the labelling of chemical substances. Therefore, the relevance of their competent risk assessment is growing regarding the use of dangerous chemical substances of an inorganic and organic nature and their anthropogenic influence.&#x0D; Aim and tasks. The paper aims to determine the formation of chemical safety competence among future specialists in therapy and rehabilitation.&#x0D; The results. A questionnaire established that future rehabilitators should acquire chemical safety competence to decipher hazard markings and possess information about the rules for working with chemicals based on a detailed study of the marking and labelling of chemical substances and rules for their use and disposal. Only 47.1% of the respondents (according to their assessment) knew the rules for handling chemicals, and 41.2% deciphered a potential danger to human health (carcinogenic effect). However, 88.2% of the higher education students interviewed wanted to develop chemical safety competence using unique chemical safety cards.&#x0D; Conclusions. The correct interpretation of the marking constituent elements allows for avoiding accidents and injuries while handling chemicals, and in the moment of a threat to human health or damage, allows the application of the given algorithm for providing first aid. Therefore, understanding the main components of chemical safety by future rehabilitators is possible through applying relevant knowledge, skills and abilities in further professional activities. However, future therapists and rehabilitators cannot correctly decipher the designation of the carcinogenic danger and do not have complete information about the rules for working with chemical substances. Therefore, it is necessary to conduct additional activities for future therapists and rehabilitators for their better understanding of the rules for handling chemicals and deciphering the dangers indicated on the labels of chemical products.

ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification.

Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.

Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery.

Nucleic acid modifications play important roles in biological activities and disease occurrences, and have been considered as cancer biomarkers. Due to the relatively low amount of nucleic acid modifications in biological samples, it is necessary to develop sensitive and reliable qualitative and quantitative methods to reveal the content of any modifications. In this review, the key processes affecting the qualitative and quantitative analyses are discussed, such as sample digestion, nucleoside extraction, chemical labeling, chromatographic separation, mass spectrometry detection, and data processing. The improvement of the detection sensitivity and specificity of analytical methods based on mass spectrometry makes it possible to study low-abundance modifications and their biological functions. Some typical nucleic acid modifications and their potential as biomarkers are displayed, and efforts to improve diagnostic accuracy are discussed. Future perspectives are raised for this research field.

Whole-Genome Mapping of Epigenetic Modification of 5-Formylcytosine at Single-Base Resolution by Chemical Labeling Enrichment and Deamination Sequencing.

DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays a critical role in a variety of biological and pathological processes in mammals. In active DNA demethylation, the 10-11 translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution is still highly desirable. Herein, we propose a chemical labeling enrichment and deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (APOBEC3A or A3A) and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mESCs. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.

Quantitative evaluation of dielectrophoretic separation efficiency of cancer exosomes based on fluorescence imaging

Liquid biopsies for cancer diagnosis using exosomes have been studied. Separating cancer cell-derived exosomes from a sample mixture is crucial, especially when they do not dominate the sample at an early stage of cancer. A method based on their electrical properties could provide a simpler separation than immune-affinity methods. We have identified the differences in electrical properties of cancerous exosomes from those of normal ones, suggesting the possibility for their dielectrophoresis (DEP) based separation. This study separated cancerous exosomes from a mixture of normal exosomes. The DEP of fluorescence-labeled exosomes suspended in aqueous media with varying electrical conductivities was investigated. The observed DEP was quantitatively evaluated using the normalization method accounting for the fluorescence fading effect. The results showed that the cancerous exosomes were preferentially concentrated under the appropriate conditions. This suggests that DEP can enable the selective capture of cancer exosomes without chemical labeling.

Analyses of plasma metabolites using a high performance four-channel CIL LC-MS method and identification of metabolites associated with enteric methane emissions in beef cattle.

Reducing enteric methane (one greenhouse gas) emissions from beef cattle not only can be beneficial in reducing global warming, but also improve efficiency of nutrient utilization in the production system. However, direct measurement of enteric methane emissions on individual cattle is difficult and expensive. The objective of this study was to detect plasma metabolites that are associated with enteric methane emissions in beef cattle. Average enteric methane emissions (CH4) per day (AVG_DAILYCH4) for each individual cattle were measured using the GreenFeed emission monitoring (GEM) unit system, and beef cattle with divergent AVG_DAILYCH4 from Angus (n = 10 for the low CH4 group and 9 for the high CH4 group), Charolais (n = 10 for low and 10 for = high), and Kinsella Composite (n = 10 for low and 10 for high) populations were used for plasma metabolite quantification and metabolite-CH4 association analyses. Blood samples of these cattle were collected near the end of the GEM system tests and a high performance four-channel chemical isotope labeling (CIL) liquid chromatography (LC) mass spectrometer (MS) method was applied to identify and quantify concentrations of metabolites. The four-channel CIL LC-MS method detected 4235 metabolites, of which 1105 were found to be significantly associated with AVG_DAILYCH4 by a t-test, while 1305 were significantly associated with AVG_DAILYCH4 by a regression analysis at p<0.05. Both the results of the t-test and regression analysis revealed that metabolites that were associated with enteric methane emissions in beef cattle were largely breed-specific whereas 4.29% to 6.39% CH4 associated metabolites were common across the three breed populations and 11.07% to 19.08% were common between two breed populations. Pathway analyses of the CH4 associated metabolites identified top enriched molecular processes for each breed population, including arginine and proline metabolism, arginine biosynthesis, butanoate metabolism, and glutathione metabolism for Angus; beta-alanine metabolism, pyruvate metabolism, glycolysis / gluconeogenesis, and citrate cycle (TCA cycle) for Charolais; phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, and arginine and proline metabolism for Kinsella Composite. The detected CH4 associated metabolites and enriched molecular processes will help understand biological mechanisms of enteric methane emissions in beef cattle. The detected CH4 associated plasma metabolites will also provide valuable resources to further characterize the metabolites and verify their utility as biomarkers for selection of cattle with reduced methane emissions.

Inside Cover Picture

Plenty of advanced methods have been developed for tracing RNA, including directly chemical RNA labeling, metabolic RNA labeling, proximity‐dependent RNA labeling, etc. These RNA labeling strategies have greatly enhanced our learning about complex roles and functions of RNA. For the deeper insight of RNA biology, there is still a constant need to develop newer RNA labeling methods. More details are discussed in the article by Weng et al. on page 790—801.image

Advancing In-Depth N-Terminomics Detection with a Cleavable 2-Pyridinecarboxyaldehyde Probe.

Proteolysis, an irreversible post-translational modification catalyzed by proteases, plays a crucial role in various biological processes. Exploring abnormally hydrolyzed proteins in pathological tissues is a valuable approach for elucidating the mechanisms underlying disease development. Herein, we have developed a cleavable 2-pyridinecarboxyaldehyde probe (2PCA-Probe) that enables efficient and in-depth N-terminomics detection, addressing limitations of previous methods. Furthermore, we unexpectedly discovered a new marker capable of identifying N-terminal chemical labeling with the 2PCA-Probe and elucidated the reaction mechanism. Using this probe, we identified 4686 N-terminal peptides in colorectal cancer and adjacent tissues, significantly expanding the depth of the N-terminome and revealing the potential role of abnormal protein hydrolysis in colorectal cancer development.

Recording physiological history of cells with chemical labeling.

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.

Recent Advance in the Study on 5‐Formylcytosine (f5C) RNA Modification

AbstractThe widespread involvement of 5‐formylcytosine f5C RNA in gene function regulation and its impact on crucial life processes like cell differentiation, embryonic development, and disease development underscores the significance of detecting this specific base modification. This detection holds great importance for basic epigenetics research and the early diagnosis and pathogenesis research of various diseases. This review aims to summarize recent research progress in f5C detection methods using selective chemical labeling, with the hope of aiding future research endeavors.

Chemical Proteomics Reveals Nε-Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization

Vibrio species, the Gram-negative bacterial pathogens causing cholera and sepsis, produce multiple secreted virulence factors for infection and pathogenesis. Among these is the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin that releases several critical effector domains with distinct functions inside eukaryotic host cells. One such effector domain, the Rho inactivation domain (RID), has been discovered to catalyze long-chain Nε-fatty-acylation on lysine residues of Rho GTPases, causing inactivation of Rho GTPases and disruption of the host actin cytoskeleton. However, whether RID modifies other host proteins to exert additional functions remains to be determined. Herein, we describe the integration of bioorthogonal chemical labeling and quantitative proteomics to globally profile the target proteins modified by RID in living cells. More than 246 proteins are identified as new RID substrates, including many involved in GTPase regulation, cytoskeletal organization, and cell division. We demonstrate that RID extensively Nε-fatty-acylates septin proteins, the fourth cytoskeletal component of mammalian cells with important roles in diverse cellular processes. While affinity purification and mass spectrometry analysis show that RID-mediated Nε-fatty-acylation does not affect septin-septin interactions, this modification increases the membrane association of septins and confers localization to detergent-resistant membrane rafts. As a result, the filamentous assembly and organization of septins are disrupted by RID-mediated Nε-fatty-acylation, further contributing to cytoskeletal and mitotic defects that phenocopy the effects of septin depletion. Overall, our work greatly expands the substrate scope and function of RID and demonstrates the role of RID-mediated Nε-fatty-acylation in manipulating septin localization and organization.

Chemical isotope labeling-assisted liquid chromatography-mass spectrometry enables sensitive and accurate determination of dipeptides and tripeptides in complex biological samples

Small peptides have attracted increasing attention for their unique features and diverse biological functions. Achieving rapid separation and accurate quantification, however, remains a challenge because of their low abundance and the co-existence of numerous structural isomers. In this study, we developed a novel approach using isotope chemical labeling for ultrasensitive determination of di/tripeptides in biological samples. We successfully synthesized a novel derivatization reagent, 4-(2-(ethoxymethylene)-3-oxobutanamido)-N,N,N-trimethylbenzenaminium iodide (EOTMBA) as well as its deuterium-labeled isotope reagent (d3-EOTMBA). A total of 97 small peptides, including 89 dipeptides and 8 tripeptides, could be completely derivatized in methanol within 1.5 h at 60°C. After EOTMBA labeling, analysis of these di/tripeptides were achieved within 22 min by LC-MS/MS analysis. The method demonstrated 86.3-113% accuracy and the limit of quantification ranged from 0.25 fmol/L to 5 nmol/L. Using this method, we achieved ultrasensitive and accurate quantification of di/tripeptides in 147 plasma, 49 urine and 46 bile samples obtained from healthy individuals and patients with biliary tract diseases. The identified differential di/tripeptide biomarker panels showed promising diagnostic performance for patients with biliary tract cancer with area under the receiver operating curve values from 0.870 to 0.996. Furthermore, this method was successfully applied to quantify di/tripeptides in the extract of an animal-derived traditional Chinese medicine, Eupolyphaga sinensis Walker. These findings highlight the possible application of the analytical method in clinics and for the purposes of quality control of traditional Chinese medicines.