Microfluidics for Peptidomics, Proteomics, and Cell Analysis

Determination of amino acids and peptides without their pre-column derivatization by capillary electrophoresis with ultraviolet and contactless conductivity detection. An overview

This review provides an overview of recent works focusing on the determination of amino acids (AAs) and peptides using capillary electrophoresis with contactless conductivity detection and ultraviolet (UV) detection, which is the most widespread detection in capillary electromigration techniques, without pre-capillary derivatization. Available options for the UV detection of these analytes, such as indirect detection, complexation with transition metal ions, and in-capillary derivatization are described. Developments in the field of direct detection of UV-absorbing AAs and peptides as well as progress in chiral separation are described. A separate section is dedicated to using on-line sample preconcentration methods combined with capillary electrophoresis-UV.

Recent developments in capillary and microchip electroseparations of peptides (2021-mid-2023)

This review article brings a comprehensive survey of developments and applications of high-performance capillary and microchip electromigration methods (zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical characterization of peptides in the period from 2021 up to ca. the middle of 2023. Progress in the study of electromigration properties of peptides and various aspects of their analysis, such as sample preparation, adsorption suppression, electroosmotic flow regulation, and detection, are presented. New developments in the particular capillary electromigration methods are demonstrated, and several types of their applications are reported. They cover qualitative and quantitative analysis of synthetic or isolated peptides and determination of peptides in complex biomatrices, peptide profiling of biofluids and tissues, and monitoring of chemical and enzymatic reactions and physicochemical changes of peptides. They include also amino acid and sequence analysis of peptides, peptide mapping of proteins, separation of stereoisomers of peptides, and their chiral analyses. In addition, micropreparative separations and physicochemical characterization of peptides and their interactions with other (bio)molecules by the above CE methods are described.

Current Challenges and Future Directions in Peptidomics

The field of peptidomics has been under development since its start more than 20 years ago. In this chapter we provide a personal outlook for future directions in this field. The applications of peptidomics technologies are spreading more and more from classical research of peptide hormones and neuropeptides towards commercial applications in plant and food-science. Many clinical applications have been developed to analyze the complexity of biofluids, which are being addressed with new instrumentation, automization, and data processing. Additionally, the newly developed field of immunopeptidomics is showing promise for cancer therapies. In conclusion, peptidomics will continue delivering important information in classical fields like neuropeptides and peptide hormones, benefiting from improvements in state-of-the-art technologies. Moreover, new directions of research such as immunopeptidomics will further complement classical omics technologies and may become routine clinical procedures. Taken together, discoveries of new substances, networks, and applications of peptides can be expected in different disciplines.

A review of acoustofluidic separation of bioparticles

Acoustofluidics is an emerging interdisciplinary research field that involves the integration of acoustics and microfluidics to address challenges in various scientific areas. This technology has proven to be a powerful tool for separating biological targets from complex fluids due to its label-free, biocompatible, and contact-free nature. Considering a careful designing process and tuning the acoustic field particles can be separated with high yield. Recently the advancement of acoustofluidics led to the development of point-of-care devices for separations of micro particles which address many of the limitations of conventional separation tools. This review article discusses the working principles and different approaches of acoustofluidic separation and provides a synopsis of its traditional and emerging applications, including the theory and mechanism of acoustofluidic separation, blood component separation, cell washing, fluorescence-activated cell sorting, circulating tumor cell isolation, and exosome isolation. The technology offers great potential for solving clinical problems and advancing scientific research.

Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics

Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.

Common Post-translational Modifications (PTMs) of Proteins: Analysis by Up-to-Date Analytical Techniques with an Emphasis on Barley

Post-translational modifications (PTMs) of biomacromolecules can be useful for understanding the processes by which a relatively small number of individual genes in a particular genome can generate enormous biological complexity in different organisms. The proteomes of barley and the brewing process were investigated by different techniques. However, their diverse and complex PTMs remain understudied. As standard analytical approaches have limitations, innovative analytical approaches need to be developed and applied in PTM studies. To make further progress in this field, it is necessary to specify the sites of modification, as well as to characterize individual isoforms with increased selectivity and sensitivity. This review summarizes advances in the PTM analysis of barley proteins, particularly those involving mass spectrometric detection. Our focus is on monitoring phosphorylation, glycation, and glycosylation, which critically influence functional behavior in metabolism and regulation in organisms.

Optimized hybrid dielectrophoretic microchip for separation of bioparticles

Point-of-care diagnostics requires a smart separation of particles and/or cells. In this work, the multiorifice fluid fractionation as a passive method and dielectrophoresis-based actuator as an active tool are combined to offer a new device for size-based particle separation. The main objective of the combination of these two well-established techniques is to improve the performance of the multiorifice fluid fractionation by taking advantage of dielectrophoresis-based actuator for separating particles. Initially, by using numerical simulations, the effect of using dielectrophoresis-based actuator in multiorifice fluid fractionation on the separation of particles was investigated, and the size of the device was optimized by 25% compared to a device without dielectrophoresis-based actuator. Also, adding dielectrophoresis-based actuator to multiorifice fluid fractionation can extend the range of flow rates needed for separation. In the absence of dielectrophoresis-based actuator, the separation took place only when the flow rate is 100 μL/min, in the presence of dielectrophoresis-based actuator (20 Vp-p), the separation happened in flow rates ranging from 70 to 120 μL/min.

Membrane-Active Peptides and Their Potential Biomedical Application

Membrane-active peptides (MAPs) possess unique properties that make them valuable tools for studying membrane structure and function and promising candidates for therapeutic applications. This review paper provides an overview of the fundamental aspects of MAPs, focusing on their membrane interaction mechanisms and potential applications. MAPs exhibit various structural features, including amphipathic structures and specific amino acid residues, enabling selective interaction with multiple membranes. Their mechanisms of action involve disrupting lipid bilayers through different pathways, depending on peptide properties and membrane composition. The therapeutic potential of MAPs is significant. They have demonstrated antimicrobial activity against bacteria and fungi, making them promising alternatives to conventional antibiotics. MAPs can selectively target cancer cells and induce apoptosis, opening new avenues in cancer therapeutics. Additionally, MAPs serve as drug delivery vectors, facilitating the transport of therapeutic cargoes across cell membranes. They represent a fascinating class of biomolecules with significant potential in basic research and clinical applications. Understanding their mechanisms of action and designing peptides with enhanced selectivity and efficacy will further expand their utility in diverse fields. Exploring MAPs holds promise for developing novel therapeutic strategies against infections, cancer, and drug delivery challenges.

[Advances in microchip electrophoresis for the separation and analysis of biological samples]

Microchip electrophoresis is a separation technology that involves fluid manipulation in a microchip; the advantages of this technique include high separation efficiency, low sample consumption, and fast and easy multistep integration. Microchip electrophoresis has been widely used to rapidly separate and analyze complex samples in biology and medicine. In this paper, we review the research progress on microchip electrophoresis, explore the fabrication and separation modes of microchip materials, and discuss their applications in the detection and analysis of biological samples. Research on microchip materials can be mainly categorized into chip materials, channel modifications, electrode materials, and electrode integration methods. Microchip materials research involves the development of silicon, glass, polydimethylsiloxane and polymethyl methacrylate-based, and paper electrophoretic materials. Microchannel modification research primarily focuses on the dynamic and static modification methods of microchannels. Although chip materials and fabrication technologies have improved over the years, problems such as high manufacturing costs, long processing time, and short service lives continue to persist. These problems hinder the industrialization of microchip electrophoresis. At present, few static methods for the surface modification of polymer channels are available, and most of them involve a combination of physical adsorption and polymers. Therefore, developing efficient surface modification methods for polymer channels remains a necessary undertaking. In addition, both dynamic and static modifications require the introduction of other chemicals, which may not be conducive to the expansion of subsequent experiments. The materials commonly used in the development of electrodes and processing methods for electrode-microchip integration include gold, platinum, and silver. Microchip electrophoresis can be divided into two modes according to the uniformity of the electric field: uniform and non-uniform. The uniform electric field electrophoresis mode mainly involves micro free-flow electrophoresis and micro zone electrophoresis, including micro isoelectric focusing electrophoresis, micro isovelocity electrophoresis, and micro density gradient electrophoresis. The non-uniform electric field electrophoresis mode involves micro dielectric electrophoresis. Microchip electrophoresis is typically used in conjunction with conventional laboratory methods, such as optical, electrochemical, and mass spectrometry, to achieve the rapid and efficient separation and analysis of complex samples. However, the labeling required for most widely used laser-induced fluorescence technologies often involves a cumbersome organic synthesis process, and not all samples can be labeled, which limits the application scenarios of laser-induced fluorescence. The applications of unlabeled microchip electrophoresis-chemiluminescence/dielectrophoresis are also limited, and simplification of the experimental process to achieve simple and rapid microchip electrophoresis remains challenging. Several new models and strategies for high throughput in situ detection based on these detection methods have been developed for microchip electrophoretic systems. However, high throughput analysis by microchip electrophoresis is often dependent on complex chip structures and relatively complicated detection methods; thus, simple high throughput analytical technologies must be further explored. This paper also reviews the progress on microchip electrophoresis for the separation and analysis of complex biological samples, such as biomacromolecules, biological small molecules, and bioparticles, and forecasts the development trend of microchip electrophoresis in the separation and analysis of biomolecules. Over 250 research papers on this field are published annually, and it is gradually becoming a research focus. Most previous research has focused on biomacromolecules, including proteins and nucleic acids; biological small molecules, including amino acids, metabolites, and ions; and bioparticles, including cells and pathogens. However, several problems remain unsolved in the field of microchip electrophoresis. Overall, microchip electrophoresis requires further study to increase its suitability for the separation and analysis of complex biological samples.

Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery

The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.

Technological advances for analyzing the content of organ-on-a-chip by mass spectrometry

Three-dimensional (3D) cell cultures, including organ-on-a-chip (OOC) devices, offer the possibility to mimic human physiology conditions better than 2D models. The organ-on-a-chip devices have a wide range of applications, including mechanical studies, functional validation, and toxicology investigations. Despite many advances in this field, the major challenge with the use of organ-on-a-chips relies on the lack of online analysis methods preventing the real-time observation of cultured cells. Mass spectrometry is a promising analytical technique for real-time analysis of cell excretes from organ-on-a-chip models. This is due to its high sensitivity, selectivity, and ability to tentatively identify a large variety of unknown compounds, ranging from metabolites, lipids, and peptides to proteins. However, the hyphenation of organ-on-a-chip with MS is largely hampered by the nature of the media used, and the presence of nonvolatile buffers. This in turn stalls the straightforward and online connection of organ-on-a-chip outlet to MS. To overcome this challenge, multiple advances have been made to pre-treat samples right after organ-on-a-chip and just before MS. In this review, we summarised these technological advances and exhaustively evaluated their benefits and shortcomings for successful hyphenation of organ-on-a-chip with MS.

Free-flow biomolecular concentration and separation of proteins and nucleic acids using teíchophoresis

The ability to preconcentrate, separate, and purify biomolecules, such as proteins and nucleic acids, is an important requirement for the next generation of portable diagnostic tools for environmental monitoring and disease detection. Traditionally, such pretreatment has been accomplished using large, centralized liquid- or solid-phase extraction equipment, which can be time-consuming and requires many processing steps. Here, we present a newly developed electrokinetic concentration technique, teíchophoresis (TPE), to concentrate and separate proteins, and to concentrate nucleic acids. In TPE, a free-flowing sample is exposed to a perpendicular electric field in the vicinity of a mass-impermeable conductive wall and a conductive terminating electrolyte (TE), which creates a high electric field strength zone between the lower mobility sample and the no-flux barrier. Unlike a similar electrokinetic concentration method, isotachophoresis (ITP), TPE does not require a leading electrolyte (LE), yet still enables a continuous field-driven electrophoretic ion migration across the channel and a free-flowing biomolecular concentration at the conductive wall. Here, we demonstrate the use of free-flow TPE (FFTPE) to manipulate biomolecular samples containing proteins or nucleic acids. We first use TPE to drive a 6.6-fold concentration increase of avidin-FITC, and also demonstrate protein separation and stacking between ovalbumin-fluorescein and BSA-AlexaFluor 555, both without the use of a conventional LE. Further, we utilize TPE to perform a 21-fold concentration increase of nucleic acids. Our results show that TPE is biocompatible with both proteins and nucleic acids, requires only 10 V DC, produces no significant sample pH changes during operation, and demonstrates that this method can be used as an effective sample pretreatment to prepare biological samples for downstream analysis in a continuous free-flowing microfluidic channel.

Peptidomics

Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.

Recent Progress and Perspectives on Neural Chip Platforms Integrating PDMS-Based Microfluidic Devices and Microelectrode Arrays

Recent years have witnessed a spurt of progress in the application of the encoding and decoding of neural activities to drug screening, diseases diagnosis, and brain-computer interactions. To overcome the constraints of the complexity of the brain and the ethical considerations of in vivo research, neural chip platforms integrating microfluidic devices and microelectrode arrays have been raised, which can not only customize growth paths for neurons in vitro but also monitor and modulate the specialized neural networks grown on chips. Therefore, this article reviews the developmental history of chip platforms integrating microfluidic devices and microelectrode arrays. First, we review the design and application of advanced microelectrode arrays and microfluidic devices. After, we introduce the fabrication process of neural chip platforms. Finally, we highlight the recent progress on this type of chip platform as a research tool in the field of brain science and neuroscience, focusing on neuropharmacology, neurological diseases, and simplified brain models. This is a detailed and comprehensive review of neural chip platforms. This work aims to fulfill the following three goals: (1) summarize the latest design patterns and fabrication schemes of such platforms, providing a reference for the development of other new platforms; (2) generalize several important applications of chip platforms in the field of neurology, which will attract the attention of scientists in the field; and (3) propose the developmental direction of neural chip platforms integrating microfluidic devices and microelectrode arrays.

Combining a hybrid chip and tube microfluidic system with fluorescent molecularly imprinted polymer (MIP) core-shell particles for the derivatisation, extraction, and detection of peptides with N-terminating phosphorylated tyrosine

The reliable identification and quantitation of phosphorylated amino acids, peptides and proteins is one of the key challenges in contemporary bioanalytical research, an area of particular interest when attempting to diagnose and treat diseases at an early stage. We have developed a synthetic probe for targeting phosphorylated amino acids, based on core-shell submicron-sized particles consisting of a silica core, coated with a molecularly imprinted polymer (MIP) shell. The MIP layer contains a fluorescent probe crosslinker which binds selectively to phosphorylated tyrosine (pY) moieties with a significant imprinting factor (IF) and responds with a "light-up" fluorescence signal. The bead-based ratiometric detection scheme has been successfully transferred to a microfluidic chip format and its applicability to rapid assays has been exemplarily shown by discriminating a pY-terminating oligopeptide against its non-phosphorylated counterpart. Such miniaturised devices could lead to an automated pY or pY N-terminated peptide measurement system in the future. The setup combines a modular microfluidic system for amino acid derivatisation, extraction (by micropillar co-flow) and selective adsorption and detection with the fluorescent MIP core-shell particle probes. A miniaturised optical assembly for low-light fluorescence measurements was also developed, based on miniaturised opto-electronic parts and optical fibres. The emission from the MIP particles upon binding of pY or pY N-terminated peptides could be monitored in real-time.

Allergy, asthma, and proteomics: opportunities with immediate impact

Allergy is widely discussed by researchers due to its complex mechanism that leads to disorders and injuries, but the reason behind the allergic status remains unclear. Current treatments are insufficient to improve the patient's quality of life significantly. New technologies in scientific and technological development are emerging. For instance, the union between allergy and peptidomics and bioinformatics tools may help fill the gaps in this field, diagnosis, and treatment. In this review, we look at peptidomics and address some findings, such as target proteins or biomarkers that help better understand mechanisms that lead to inflammation, organ damage, and, consequently, poor quality of life or even death.

Oscillatory Motion of Water Droplets Both in Oil and on Superhydrophobic Surface under Corona Discharge

Charged droplets driven by Coulomb force are an important part of a droplet-based micro reactor. In this study, we realized the rapid oscillatory motion of droplets both in oil and on superhydrophobic surface by injecting charges through corona discharge. Distinct from the oscillatory motion of water droplets under a DC electric field, charge injection can make the motion of water droplets more flexible. A droplet in the oil layer can move up and down regularly under the action of corona discharge, and the discharge voltage can control the movement period and height of the droplet. In addition, the left-right translation of droplets on a superhydrophobic surface can be achieved by injecting charges into the hydrophobic film surface through corona discharge. Two kinds of droplet motion behaviors are systematically analyzed, and the mechanism of droplet motion is explained. The present results could help establish new approaches to designing efficient machines in microfluidics and micromechanical equipment.

From Microtiter Plates to Droplets—There and Back Again

Droplet-based microfluidic screening techniques can benefit from interfacing established microtiter plate-based screening and sample management workflows. Interfacing tools are required both for loading preconfigured microtiter-plate (MTP)-based sample collections into droplets and for dispensing the used droplets samples back into MTPs for subsequent storage or further processing. Here, we present a collection of Digital Microfluidic Pipetting Tips (DMPTs) with integrated facilities for droplet generation and manipulation together with a robotic system for its operation. This combination serves as a bidirectional sampling interface for sample transfer from wells into droplets (w2d) and vice versa droplets into wells (d2w). The DMPT were designed to fit into 96-deep-well MTPs and prepared from glass by means of microsystems technology. The aspirated samples are converted into the channel-confined droplets’ sequences separated by an immiscible carrier medium. To comply with the demands of dose-response assays, up to three additional assay compound solutions can be added to the sample droplets. To enable different procedural assay protocols, four different DMPT variants were made. In this way, droplet series with gradually changing composition can be generated for, e.g., 2D screening purposes. The developed DMPT and their common fluidic connector are described here. To handle the opposite transfer d2w, a robotic transfer system was set up and is described briefly.

Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes

Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.

Recent developments in capillary and microchip electroseparations of peptides (2019-mid 2021)

The review provides a comprehensive overview of developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, microscale isolation, and physicochemical characterization of peptides from 2019 up to approximately the middle of 2021. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis, such as sample preparation, sorption suppression, EOF control, and detection, are presented. New developments in the individual CE and CEC methods are demonstrated and several types of their applications are shown. They include qualitative and quantitative analysis, determination in complex biomatrices, monitoring of chemical and enzymatic reactions and physicochemical changes, amino acid, sequence, and chiral analyses, and peptide mapping of proteins. In addition, micropreparative separations and determination of significant physicochemical parameters of peptides by CE and CEC methods are described.

Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression

Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.

Proteomic Exploration of Plasma Exosomes and Other Small Extracellular Vesicles in Pediatric Hodgkin Lymphoma: A Potential Source of Biomarkers for Relapse Occurrence

Exosomes and other small extracellular vesicles (EVs) are potential sources of cancer biomarkers. Plasma-derived EVs have not yet been studied in pediatric Hodgkin lymphoma (HL), for which predictive biomarkers of relapse are greatly needed. In this two-part proteomic study, we used two-dimensional difference gel electrophoresis (2D-DIGE) followed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to analyze EV proteins of plasma collected at diagnosis from children with nodular sclerosis HL, relapsed or not. EVs isolated using membrane affinity had radii ranging from 20 to 130 nm and contained the programmed cell death 6-interacting (ALIX) and the tumor susceptibility gene 101 (TSG101) proteins, whereas calnexin (CANX) was not detected. 2D-DIGE identified 16 spots as differentially abundant between non-relapsed and relapsed HL (|fold change| ≥ 1.5, p < 0.05). LC–MS/MS identified these spots as 11 unique proteins, including five more abundant in non-relapsed HL (e.g., complement C4b, C4B; fibrinogen γ chain, FGG) and six more abundant in relapsed HL (e.g., transthyretin, TTR). Shotgun LC–MS/MS on pooled EV proteins from non-relapsed HL identified 161 proteins, including 127 already identified in human exosomes (ExoCarta data). This EV cargo included 89 proteins not yet identified in exosomes from healthy plasma. Functional interrogation by the Database for Annotation, Visualization and Integrated Discovery (DAVID) revealed that the EV proteins participate in platelet degranulation and serine-type endopeptidase activity as the most significant Gene Ontology (GO) biological process and molecular function (p < 0.01).