Different Types Of Biomolecules Research Articles

Identification of novel biomarker hsa_circ_0003914 for rheumatoid arthritis from plasma exosomes

Rheumatoid arthritis (RA) is a complex autoimmune disease featuring invasive and infiltrative fibroblast-like synoviocytes (FLS) that lead to joint damage. While current RA pathological mechanisms remain incompletely defined, exosomes have been implicated as having the potential to drive disease progression due to their ability to deliver different types of biomolecules to tissues effected by RA. One potentially disease exacerbating molecule type found in exosomes are Circular RNAs (circRNAs), which are highly stable and have been previously implicated in RA pathogenesis. Here, we examine hsa_circ_0003914, a circRNA found in exosomes located in blood plasma, for a role in RA. Plasma exosomes were isolated and injected into collagen-induced arthritis (CIA) mice, followed by functional experiments to analyze the influence of exosomes on FLS formation. Sequencing revealed the presence of hsa_circ_0003914 in exosomes, so we examined its association with clinical markers in RA. Finally, the role for hsa_circ_0003914 in RA was directly confirmed through in vivo and in vitro experiments. We found that plasma exosomes isolated from RA patients could aggravate the disease of CIA mice, compared to exosomes isolated from healthy control patients. Hsa_circ_0003914 was highly enriched in the exosomes of RA patients. Mechanistically, Hsa_circ_0003914 promoted abnormal cell proliferation, migration, invasion and stimulated the secretion of inflammatory cytokines in FLSs through targeting NF-κB/p65 signaling pathway. Interestingly, knockdown of hsa_circ_0003914 rescued disease phenotypes in CIA mice. Taken together, these data implicate hsa_circ_0003914 as a potential therapeutic target for the prevention and management of RA.

The Gas Chromatography Mass Spectrometry Analysis of an Ayurvedic Formulation Amruthadi Kashaya

Amruthadi Kashaya is a Ayurvedic formulation mentioned in the book Arogya Kalpadruma for the treatment of Pandu (anaemic syndrome), Kamala (jaundice) and Raktapitha (bleeding disorders). The Yoga contains six drugs namely Amrutha (Tinospora cordifolia), Vasa (Adhatoda vasica), Yashtimadhu (Glycyrrhiza glabra), Tiktha (Solanum anguivi), Ela (Elettaria cardamomum), Pichumantha (Azadirachta indica). This Kashaya is rich in phytoconstituents, such as phenolics, terpenoids, and lipids, which are known for their many biological benefits, including anti-inflammatory, anti-cancer, and antioxidant effects. The purpose of the current study is to use Gas Chromatography Mass Spectrometry (GCMS) analysis to identify the different types of bio molecules that are present in this Kashaya. Kashaya was prepared according to standard protocol. It was concentrated in the rotary vacuum evaporator, and the total soluble solid (TSS) obtained was used for GCMS analysis. The GCMS of Kashaya showed the presence of bio molecules such as 7 Hexadecanoic acid, methyl ester, Methyl tetradecanoate, Diethyl Phthalate, Dodecanoic acid, methyl ester, Methyl stearate, à-Terpineol, Methyl 8-methylnonanoate, 3-Cyclohexene-1-methanol, à, à,4-trimethyl-, acetate, Decanoic acid, methyl ester, 1,6,10-Dodecatrien-3-ol,3,7,11-trimethyl-, (E)-, Ethyl iso-allocholate, Spiro [2,4] hepta-4,6-diene, Butylated Hydroxytoluene, 9-Hexadecenoic acid, methyl ester, (Z) etc. à-Terpineol, 7-Hexadecenoic acid, methyl ester, Butylated hydroxytoluene, Nerolidyl acetate have antioxidant activity likewise some of the bio molecules have anti-inflammatory, antibacterial, anticancer activity. It is concluded that Ayurvedic formulation Amruthadi Kashaya contains many bio molecules having therapeutic actions.

USING FOURIER TRANSFER INFRARED SPECTROSCOPY TO ANALYSIS EFFECTS OF CADMIUM TREATMENT ON RICE (ORYZA SATIVA L.) SEEDLINGS

The present study is aimed to analyse the DMSO (Dimethyl sulfoxide) extract of shoots and roots of Oryza sativaL. (var IET 4786) through FTIR spectroscopy method. These studies contain different characteristic of the peak values with various functional compounds in the extracts. This analysis revealed the presence of different types of biomolecules in plant extracts. The FTIR analysis of DMSO leaf extracts of Oryza sativaL. confirmed the presence of alcohols, phenols, amides, alkanes, carboxylic acids, aldehydes, ketones, alkenes, aromatics, esters, alkyl halides and aliphatic amines compounds each of the functional group showed major peaks. This method was performed on a spectrophotometer system which was used to detect the characteristics peak values and their functional groups. In this present study, the FTIR spectrum profile for the plant Oryza sativa L. is generated andcan be used in the industry.

Exosomes in Cancer: Diagnostic and Therapeutic Applications.

Small extracellular vesicles called exosomes are produced by cells and contain a range of biomolecules, including proteins, lipids, and nucleic acids. Exosomes have been implicated in the development and spread of cancer, and recent studies have shown that their contents may be exploited as biomarkers for early detection and ongoing surveillance of the disease. In this review article, we summarize the current knowledge on exosomes as biomarkers of cancer. We discuss the various methods used for exosome isolation and characterization, as well as the different types of biomolecules found within exosomes that are relevant for cancer diagnosis and prognosis. We also highlight recent studies that have demonstrated the utility of exosomal biomarkers in different types of cancer, such as lung cancer, breast cancer, and pancreatic cancer. Overall, exosomes show great promise as noninvasive biomarkers for cancer detection and monitoring. Exosomes have the ability to transform cancer diagnostic and therapeutic paradigms, providing promise for more efficient and individualized. This review seeks to serve as an inspiration for new ideas and research in the never-ending fight against cancer. Moreover, further studies are needed to validate their clinical utility and establish standardized protocols for their isolation and analysis. With continued research and development, exosomal biomarkers have the potential to revolutionize cancer diagnosis and treatment.

A Direct Immunoassay Based on Surface-Enhanced Spectroscopy Using AuNP/PS-b-P2VP Nanocomposites

A biosensor was developed for directly detecting human immunoglobulin G (IgG) and adenosine triphosphate (ATP) based on stable and reproducible gold nanoparticles/polystyrene-b-poly(2-vinylpyridine) (AuNP/PS-b-P2VP) nanocomposites. The substrates were functionalized with carboxylic acid groups for the covalent binding of anti-IgG and anti-ATP and the detection of IgG and ATP (1 to 150 μg/mL). SEM images of the nanocomposite show 17 ± 2 nm AuNP clusters adsorbed over a continuous porous PS-b-P2VP thin film. UV–VIS and SERS were used to characterize each step of the substrate functionalization and the specific interaction between anti-IgG and the targeted IgG analyte. The UV–VIS results show a redshift of the LSPR band as the AuNP surface was functionalized and SERS measurements showed consistent changes in the spectral features. Principal component analysis (PCA) was used to discriminate between samples before and after the affinity tests. Moreover, the designed biosensor proved to be sensitive to different concentrations of IgG with a limit-of-detection (LOD) down to 1 μg/mL. Moreover, the selectivity to IgG was confirmed using standard solutions of IgM as a control. Finally, ATP direct immunoassay (LOD = 1 μg/mL) has demonstrated that this nanocomposite platform can be used to detect different types of biomolecules after proper functionalization.

Green fabrication of zinc oxide nanoparticles by Anagallis arvensis ethanolic extract and their antibacterial properties

Green approach of zinc oxide nanoparticle fabrication is a reliable reaction that has compatibility with many biological properties. In the present study the approach of zinc oxide nanoparticle has been synthesized by A. arvensis aerial part using ethanol extract. The morphological, compositional and structural properties have been investigated by SEM, XRD, and FTIR studies. XRD technique demonstrated the crystallite size of 17nm with the help of Debye-Scherrer's equation which was obtained in nanorange. SEM technique demonstrated their microscopic agglomerated crystal image of green synthesizes metal in zinc oxide nanoparticle. FTIR technique represents the different types of biomolecules i.e. phenol, alkynes etc. that are responsible for good nanoparticle fabrication. These biomolecules work as encapsulation and stabilization agents for nanoparticle fabrication. These all properties of nanoparticle fabrication have been responsible for the antimicrobial activity.

Advances in Biohybridized Planar Polymer Membranes and Membrane‐Like Matrices

AbstractThe past few decades have seen increasing growth in the field of biomimetic membranes and thus also a rapid expansion of their biomedical and technological applications. Versatility, stability and scalability have moved biohybrid polymer membranes into the limelight. This review focuses on planar, soft polymer membranes and polymer‐based matrices and their role as a host for different types of biomolecules. Because biomimetic polymer platforms present an extensive, ever‐growing field, we limit ourselves mostly to the discussion of producing planar polymer membranes on solid supports that lend themselves to functionalization by biomolecules. We present an overview of the major highlights and challenges associated with the biohybridization of such polymer platforms. In particular, we elaborate on procedures developed to maintain optimal peptide and membrane protein performance in a customized polymer membrane or membrane‐like environment. Finally, we discuss a number of applications of such biohybridized polymer platforms and contemplate future developments to further exploit their potential.

Exploring the Reactivity of Polyoxometalates toward Proteins: From Interactions to Mechanistic Insights.

The latest advances in the study of the reactivity of metal-oxo clusters toward proteins showcase how fundamental insights obtained so far open new opportunities in biotechnology and medicine. In this Perspective, these studies are discussed through the lens of the reactivity of a family of soluble anionic metal-oxo nanoclusters known as polyoxometalates (POMs). POMs act as catalysts in a wide range of reactions with several different types of biomolecules and have promising therapeutic applications due to their antiviral, antibacterial, and antitumor activities. However, the lack of a detailed understanding of the mechanisms behind biochemically relevant reactions-particularly with complex biological systems such as proteins-still hinders further developments. Hence, in this Perspective, special attention is given to reactions of POMs with peptides and proteins showcasing a molecular-level understanding of the reaction mechanism. In doing so, we aim to highlight both existing limitations and promising directions of future research on the reactivity of metal-oxo clusters toward proteins and beyond.

Curvature induced structural changes of the chicken villin headpiece subdomain by single walled carbon nanotubes.

Carbon nanotubes (CNTs) are identified as potential candidates for drug and biomolecular loading and delivery. CNTs of different chiralities have different diameters, which may significantly affect their abilities to interact with different types of biomolecules. Herein, we employ classical molecular dynamics simulation to provide insight into the curvature-dependent interactions between a model protein, chicken villin headpiece subdomain (HP36), with CNTs having chiralities (8,8), (12,12), and (20,20). It is revealed that, with increasing radii, the protein encounters more aromatic carbon atoms on the surface of the CNT, leading to its increasing strength of adsorption. However, the extent of adsorption has a limiting magnitude, after which an increase in the radius of the nanotube has practically no effect on the extent of adsorption. Spontaneous encapsulation of the protein was demonstrated using a (28,28) CNT, where the protein is found to undergo insignificant structural perturbation. Finally, steered molecular dynamics simulations have been performed to mimic the force-induced release of the protein from within the nanotube cavity. It has been identified that a minimum force of ∼300 pN and a minimum velocity of 4 Å ns-1 are required to release the protein from the CNT at 300 K. Any external force below the critical magnitude and inducing velocity less than 4 Å ns-1 allows the translocation of the protein through the inner surface of the CNT; however, before being released, the protein undergoes unfolding, thereby losing the secondary structure and biological activity.

Fallopian tube secreted protein affects ovarian metabolites in high grade serous ovarian cancer.

High grade serous ovarian cancer (HGSOC), the most lethal histotype of ovarian cancer, frequently arises from fallopian tube epithelial cells (FTE). Once transformed, tumorigenic FTE often migrate specifically to the ovary, completing the crucial primary metastatic step and allowing the formation of the ovarian tumors after which HGSOC was originally named. As only the fimbriated distal ends of the fallopian tube that reside in close proximity to the ovary develop precursor lesions such as serous tubal intraepithelial carcinomas, this suggests that the process of transformation and primary metastasis to the ovary is impacted by the local microenvironment. We hypothesize that chemical cues, including small molecules and proteins, may help stimulate the migration of tumorigenic FTE to the ovary. However, the specific mediators of this process are still poorly understood, despite a recent growth in interest in the tumor microenvironment. Our previous work utilized imaging mass spectrometry (IMS) to identify the release of norepinephrine (NE) from the ovary in co-cultures of tumorigenic FTE cells with an ovarian explant. We predicted that tumorigenic FTE cells secreted a biomolecule, not produced or produced with low expression by non-tumorigenic cells, that stimulated the ovary to release NE. As such, we utilized an IMS mass-guided bioassay, using NE release as our biological marker, and bottom-up proteomics to demonstrate that a secreted protein, SPARC, is a factor produced by tumorigenic FTE responsible for enhancing release of ovarian NE and influencing primary metastasis of HGSOC. This discovery highlights the bidirectional interplay between different types of biomolecules in the fallopian tube and ovarian microenvironment and their combined roles in primary metastasis and disease progression.

Uncovering the Interaction between Intracellular Telomerase Activity and Hydrogen Peroxide during Cancer Cell Apoptosis Utilizing a Dual-Color Fluorescent Nanoprobe.

Uncovering the intrinsic interaction of different bioactive species, i.e., reactive oxygen species (ROS) and telomerase, is of great importance because they play interrelated and interdependent biological roles in living organisms. Nevertheless, exploration of the intracellular ROS/telomerase cross-talk by effective and noninvasive methods remains a great challenge, as it is difficult to simultaneously detect different types of biomolecules (i.e., active small molecules and proteins) in living cells. To address this issue, herein, we report, for the first time, a novel fluorescent nanoprobe for simultaneous determination and in situ imaging of telomerase activity and hydrogen peroxide (H2O2) in living cells. With the advantage of high sensitivity and good specificity, this newly fabricated nanoprobe was successfully applied to precisely visualize and monitor the changes in telomerase activity and H2O2 concentration in cancer cells. More significantly, by employing the nanoprobe as a one-step incubation tool, it is found that there is a cross-talk between H2O2 and telomerase activity in the drug-induced cancer cells' apoptosis process, which provides valuable information for gaining fundamental insights into the relationship between ROS and telomerase activity in cancer treatments. This work affords a promising method for revealing the relevant regulatory mechanisms and roles of ROS and telomerase activity in the occurrence, evolvement, and treatment of diseases.

SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks

BackgroundRepresenting the complex interplay between different types of biomolecules across different omics layers in multi-omics networks bears great potential to gain a deep mechanistic understanding of gene regulation and disease. However, multi-omics networks easily grow into giant hairball structures that hamper biological interpretation. Module detection methods can decompose these networks into smaller interpretable modules. However, these methods are not adapted to deal with multi-omics data nor consider topological features. When deriving very large modules or ignoring the broader network context, interpretability remains limited. To address these issues, we developed a SUbgraph BAsed mulTi-OMIcs Clustering framework (SUBATOMIC), which infers small and interpretable modules with a specific topology while keeping track of connections to other modules and regulators.ResultsSUBATOMIC groups specific molecular interactions in composite network subgraphs of two and three nodes and clusters them into topological modules. These are functionally annotated, visualized and overlaid with expression profiles to go from static to dynamic modules. To preserve the larger network context, SUBATOMIC investigates statistically the connections in between modules as well as between modules and regulators such as miRNAs and transcription factors. We applied SUBATOMIC to analyze a composite Homo sapiens network containing transcription factor-target gene, miRNA-target gene, protein–protein, homologous and co-functional interactions from different databases. We derived and annotated 5586 modules with diverse topological, functional and regulatory properties. We created novel functional hypotheses for unannotated genes. Furthermore, we integrated modules with condition specific expression data to study the influence of hypoxia in three cancer cell lines. We developed two prioritization strategies to identify the most relevant modules in specific biological contexts: one considering GO term enrichments and one calculating an activity score reflecting the degree of differential expression. Both strategies yielded modules specifically reacting to low oxygen levels.ConclusionsWe developed the SUBATOMIC framework that generates interpretable modules from integrated multi-omics networks and applied it to hypoxia in cancer. SUBATOMIC can infer and contextualize modules, explore condition or disease specific modules, identify regulators and functionally related modules, and derive novel gene functions for uncharacterized genes. The software is available at https://github.com/CBIGR/SUBATOMIC.

Virus-like Particles as Nanocarriers for Intracellular Delivery of Biomolecules and Compounds

Virus-like particles (VLPs) are nanostructures assemble from viral proteins. Besides widely used for vaccine development, VLPs have also been explored as nanocarriers for cargo delivery as they combine the key advantages of viral and non-viral vectors. While it protects cargo molecules from degradation, the VLP has good cell penetrating property to mediate cargo passing the cell membrane and released into cells, making the VLP an ideal tool for intracellular delivery of biomolecules and drugs. Great progresses have been achieved and multiple challenges are still on the way for broad applications of VLP as delivery vectors. Here we summarize current advances and applications in VLP as a delivery vector. Progresses on delivery of different types of biomolecules as well as drugs by VLPs are introduced, and the strategies for cargo packaging are highlighted which is one of the key steps for VLP mediated intracellular delivery. Production and applications of VLPs are also briefly reviewed, with a discussion on future challenges in this rapidly developing field.

Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective.

Clostridioides difficile (C. difficile), known as the major cause of antibiotic-associated diarrhea, is regarded as one of the most common healthcare-associated bacterial infections worldwide. Due to the emergence of hypervirulent strains, development of new therapeutic methods for C. difficile infection (CDI) has become crucially important. In this context, antibodies have been introduced as valuable tools in the research and clinical environments, as far as the effectiveness of antibody therapy for CDI was reported in several clinical investigations. Hence, production of high-performance antibodies for treatment of CDI would be precious. Traditional approaches of antibody generation are based on hybridoma technology. Today, application of in vitro technologies for generating recombinant antibodies, like phage display, is considered as an appropriate alternative to hybridoma technology. These techniques can circumvent the limitations of the immune system and they can be exploited for production of antibodies against different types of biomolecules in particular active toxins. Additionally, DNA encoding antibodies is directly accessible in in vitro technologies, which enables the application of antibody engineering in order to increase their sensitivity and specificity. Here, we review the application of antibodies for CDI treatment with an emphasis on recombinant fragment antibodies. Also, this review highlights the current and future prospects of the aforementioned approaches for antibody-mediated therapy of CDI.

Formation, contents, functions of exosomes and their potential in lung cancer diagnostics and therapeutics.

Lung cancer is the leading cause of cancer‐related death worldwide due to diagnosis in the advanced stage and drug resistance in the subsequent treatments. Development of novel diagnostic and therapeutic methods is urged to improve the disease outcome. Exosomes are nano‐sized vehicles which transport different types of biomolecules intercellularly, including DNA, RNA and proteins, and are implicated in cross‐talk between cells and their surrounding microenvironment. Tumor‐derived exosomes (TEXs) have been revealed to strongly influence the tumor microenvironment, antitumor immunoregulatory activities, tumor progression and metastasis. Potential of TEXs as biomarkers for lung cancer diagnosis, prognosis and treatment prediction is supported by numerous studies. Moreover, exosomes have been proposed to be promising drug carriers. Here, we review the mechanisms of exosomal formation and uptake, the functions of exosomes in carcinogenesis, and potential clinical utility of exosomes as biomarkers, tumor vaccine and drug delivery vehicles in the diagnosis and therapeutics of lung cancer.

Interactions between long non‑coding RNAs and RNA‑binding proteins in cancer (Review).

Long non-coding RNAs (lncRNAs) fulfill important roles in the majority of cellular processes. Previous studies have demonstrated that lncRNAs are involved in the pathogenesis of various diseases, including cancer. However, to date, the functions of only a small number of the known lncRNAs have been well-documented. lncRNAs comprise a class of multifunctional non-coding transcripts that are able to interact with different types of biomolecules. Interactions between lncRNAs and RNA-binding proteins (RBPs) provide an important mechanism through which lncRNAs exert their regulatory functions, mainly through findings on ‘generalized RBPs’. Regulatory effects on lncRNAs mediated by RBPs have also been explored. Taking account of the research that has been completed to date, the continued and in-depth study of the bidirectional interactions between lncRNAs and RBPs will prove to be of major importance for understanding the pathogenesis of cancer and for developing effective therapies. The present review aims to explore the interactions between lncRNAs and RBPs that have been investigated in cancer, taking into consideration several different aspects, including the regulation of expression, subcellular localization and the mediation of diverse functions.

Quantifying full-length circular RNAs in cancer.

Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.

Redox-Mediated Regulation of Mitochondrial Biogenesis, Dynamics, and Respiratory Chain Assembly in Yeast and Human Cells.

Mitochondria are double-membrane organelles that contain their own genome, the mitochondrial DNA (mtDNA), and reminiscent of its endosymbiotic origin. Mitochondria are responsible for cellular respiration via the function of the electron oxidative phosphorylation system (OXPHOS), located in the mitochondrial inner membrane and composed of the four electron transport chain (ETC) enzymes (complexes I-IV), and the ATP synthase (complex V). Even though the mtDNA encodes essential OXPHOS components, the large majority of the structural subunits and additional biogenetical factors (more than seventy proteins) are encoded in the nucleus and translated in the cytoplasm. To incorporate these proteins and the rest of the mitochondrial proteome, mitochondria have evolved varied, and sophisticated import machineries that specifically target proteins to the different compartments defined by the two membranes. The intermembrane space (IMS) contains a high number of cysteine-rich proteins, which are mostly imported via the MIA40 oxidative folding system, dependent on the reduction, and oxidation of key Cys residues. Several of these proteins are structural components or assembly factors necessary for the correct maturation and function of the ETC complexes. Interestingly, many of these proteins are involved in the metalation of the active redox centers of complex IV, the terminal oxidase of the mitochondrial ETC. Due to their function in oxygen reduction, mitochondria are the main generators of reactive oxygen species (ROS), on both sides of the inner membrane, i.e., in the matrix and the IMS. ROS generation is important due to their role as signaling molecules, but an excessive production is detrimental due to unwanted oxidation reactions that impact on the function of different types of biomolecules contained in mitochondria. Therefore, the maintenance of the redox balance in the IMS is essential for mitochondrial function. In this review, we will discuss the role that redox regulation plays in the maintenance of IMS homeostasis as well as how mitochondrial ROS generation may be a key regulatory factor for ETC biogenesis, especially for complex IV.

Development of a HPLC-MS/MS method for assessment of thiol redox status in human tear fluids

Oxidative stress is reported to be part of the pathology of many ocular diseases. For the diagnosis of ocular diseases, tear fluid has unique advantages. Although numerous analytical methods exist for the measurement of different types of biomolecules in tear fluid, few have been reported for comprehensive understanding of oxidative stress-related thiol redox signaling. In this study, a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method was developed to determine a panel of twelve metabolites that systematically covered several thiol metabolic pathways. With optimization of MS/MS parameters and HPLC mobile phases, this method was sensitive (LOQ as low as 0.01 ng/ml), accurate (80–125% spike recovery) and precise (<10% RSD). This LC-MS/MS method combined with a simple tear fluid collection with Schirmer test strip followed by ultrafiltration allowed the high-throughput analysis for efficient determination of metabolites associated with thiol redox signaling in human tear fluids. The method was then applied to a small cohort of tear fluids obtained from healthy individuals. The method presented here provides a new technique to facilitate future work aiming to determine the complex thiol redox signaling in tear fluids for accurate assessment and diagnosis of ocular diseases.

Three-in-One Simultaneous Extraction of Proteins, Metabolites and Lipids for Multi-Omics.

Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics, and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical properties. Therefore, several sets/aliquots of samples are needed for extracting different molecules. Here we adapted a biphasic fractionation method to extract proteins, metabolites, and lipids from the same sample (3-in-1) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) multi-omics. To demonstrate utility of the improved method, we used bacteria-primed Arabidopsis leaves to generate multi-omics datasets from the same sample. In total, we were able to analyze 1849 proteins, 1967 metabolites, and 424 lipid species in single samples. The molecules cover a wide range of biological and molecular processes, and allow quantitative analyses of different molecules and pathways. Our results have shown the clear advantages of the multi-omics method, including sample conservation, high reproducibility, and tight correlation between different types of biomolecules.