Absolute and relative quantification of multiplex DNA assays based on an elemental labeling strategy

ICP-MS based detection method combined with Au NP and Ag NP labeling for bacteremia diagnosis

Bacteremia, as a serious infectious disease, has an increasing incidence and a high mortality rate. Early diagnosis and early treatment are crucial for improving the cure rate. In this work, we proposed an inductively coupled plasma mass spectrometry (ICP-MS)-based detection method combined with gold nanoparticle (Au NP) and silver nanoparticle (Ag NP) labeling for the simultaneous detection of Salmonella and Escherichia coli (E. coli O157:H7) in human blood samples. Salmonella and E. coli O157:H7 were captured by magnetic beads coupled with anti-8G3 and anti-7C2, and then specifically labeled by Au NP-anti-5H12 and Ag NP-anti-8B1 respectively, which were used as signal probes for ICP-MS detection. Under the optimal experimental conditions, the limits of detection of 164 CFU mL-1 for Salmonella, 220 CFU mL-1for E. coli O157:H7 and the linear ranges of 400-80,000 CFU mL-1Salmonella, 400-60,000 CFU mL-1 E. coli O157:H7 were obtained. The proposed method can realize the simultaneous detection of two types of pathogenic bacteria in human whole blood in 3.5 h, showing great potential for the rapid diagnosis of bacteremia in clinic.

Single Particle Analysis-Enhanced DNA Walking Machine for Sensitive miRNA Detection

DNA walking machines have achieved significant breakthroughs in areas such as biosensing, bioimaging, and early cancer diagnosis, facilitated by the self-assembly of DNA or its combination with other materials, such as magnetic beads and metal nanoparticles. However, current DNA walking machine strategies are constantly challenged by inadequate analytical sensitivity, while sophisticated signal amplification procedures are often indispensable. Single-particle inductively coupled plasma mass spectrometry (SP-ICPMS) provides superior sensitivity and can effectively discriminate between background noise and detected signals due to the large number of metal atoms in a nanoparticle and the concentrating effect of single nanoparticle detection. In this study, we present a novel approach utilizing single nanoparticle counting and duplex-specific nuclease (DSN)-assisted signal amplification to construct a 3D DNA walking machine for detecting the aggressive prostate cancer (PCa) biomarker miRNA-200c. The proposed strategy showed an improvement in sensitivity with a detection limit (LOD) of 0.93 pM (28 amol) and was successfully applied in human serum samples. To the best of our knowledge, this is the first report of the DNA walking machine with single nanoparticle counting study.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS)

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

Simplified Rapid Enrichment of CTCs and Selective Recognition Prereduction Enable a Homogeneous ICP-MS Liquid Biopsy Strategy of Lung Cancer

The effective enrichment and hypersensitivity analysis of circulating tumor cells (CTCs) in clinical whole blood samples are highly significant for clinical tumor liquid biopsy. In this study, we established an easy operation and affordable CTCs extraction technique while simultaneously performing the homogeneous inductively coupled plasma mass spectrometry (ICP-MS) determination of CTCs in lung cancer clinical samples based on selective recognition reactions and prereduction phenomena. Our strategy allowed for the pretreatment of whole blood samples in less than 45 min after step-by-step centrifugation, which only required lymphocyte separation solution and erythrocyte lysate. Furthermore, a three-stage signal amplification system consisting of catalytic hairpin assembly (CHA), selective recognition for C-Ag+-C structures and Ag+ of copper sulfide nanoparticles (CuS NPs), and prereduction of Hg2+ through ascorbic acid (AA) was constructed by using mucin 1 as the CTCs marker and the aptamer for identification probes. In optimal conditions, the detection limits of ICP-MS were as low as 0.3 ag/mL for mucin 1 and 0.25 cells/mL for A549 cells. This method analyzed CTCs in 58 clinical samples quantitatively, and the results were consistent with clinical CT images and pathological findings. The area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was 0.957, which provided a specificity of 100% and a sensitivity of 91.5% for the assay. Therefore, the simplicity of the extraction method, the accessibility, and the high sensitivity of the assay method make the strategies attractive for clinical CTCs testing applications.

Single Cell Phenotypic Analysis for Cancer Stem Cell Identification by Dual-Isotope ICP-QMS

Single cell phenotypic analysis is significant for clinical diagnosis, treatment, and prognosis of cancer. Accurate differentiation of cancer stem cell (CSC) subpopulations from a large number of cancer cells may become a cancer surveillance tool and provide important implications for the development of new CSC-targeted therapy strategies. Herein, we report a new approach based on dual-isotope inductively coupled plasma quadrupole mass spectrometry (ICP-QMS) for single cell phenotypic analysis. High-throughput single cell sampling was achieved by a spiral channel microfluidic chip for cell focusing and alignment, and single cell analysis was performed with time-resolved ICP-QMS by identifying the highly specific probes. This enables the monitoring of two surface protein markers (EpCAM and MUC1) of three cell types, i.e., HeLa, MCF-7, and HepG2, at single cell level. The analysis of breast cancer stem cells further confirmed its capability in distinguishing rare cell phenotypes. The present study provides promising possibilities for adopting ICP-QMS in biomedical investigations in terms of cell typing, stemness identification of tumor cells, and cell heterogeneity analysis.

Isotope-encoded tetrahedral DNA for multiple SARS-CoV-2 variant diagnosis

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an unprecedented demand for accurate and cost-effective diagnostic assays to discriminate between different variants. Whilst many bioassays have been successfully demonstrated for SARS-CoV-2 detection, diagnosis of its variants remains challenging and mainly relies on time-consuming and costly sequencing techniques. Herein, we proposed a triplevalent tetrahedral DNA nanostructure (tTDN) with three overhang isotope probes capable of multiplex simultaneous analysis. HV69/70 del (alpha-specific), K417N (beta-specific) and T478K (delta-specific) and omicron with common mutations above of the SARS-CoV-2 S gene were detected selectively with the aid of the TDN scaffold and MNAzyme system, and a sensitive strategy enabling the screening of four kinds of variants of concern (VOC) was achieved.

Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules

Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.

Mass Spectrometric Multiplex Detection of MicroRNA and Protein Biomarkers for Liver Cancer

The occurrence of cancers is often accompanied by the abnormal expression of several sorts of biomarkers (e.g., nucleic acids and proteins). The multiplex assessment of them would substantially aid in the early detection and precise diagnosis, which is often hampered by their different detection schemes, different reaction matrix and reagents, and spectral overlapping. Herein, we propose a simple and sensitive mass spectrometric method for the multiplex detection of nucleic acid and protein, in which liver cancer-related biomarkers miRNA 223 and alpha-fetoprotein (AFP) were selected as model analytes. The self-amplification effect of metal atom-based nanoparticle probes can provide high sensitivity in complex serum samples without any additional amplification procedure. The detection limits for the simultaneous detection of miRNA 223 and AFP were 103 (2.1 pM) and 219 amol (0.15 ng/mL), respectively, with high specificity and selectivity. The proposed method is potentially useful for the rapid screening of cancers.

Simple Amplifier Coupled with a Lanthanide Labeling Strategy for Multiplexed and Specific Quantification of MicroRNAs

Inductively coupled plasma-mass spectrometry (ICP-MS) with elemental labeling is a promising strategy for multiplex microRNA (miRNA) analysis. However, it is still challenging for specific analysis of multiple miRNAs with high homology, and the development of multiplex assays is always limited by the complexity of the sequence design. Herein, a simple and direct ICP-MS-based assay was developed for the simultaneous detection of three miRNAs by combining the lanthanide labeling strategy with entropy-driven catalytic (EDC) amplification. Owing to the specificity of EDC for nucleic acid recognition, it is able to differentiate miRNAs with single-base mutation in each EDC circuit. A universal biotin-labeled DNA strand was designed to hybridize with the DNA substrates for three EDC circuits, targeting miRNA-21, miRNA-155, and miRNA-10b, respectively. All the substrates were loaded on the surface of streptavidin magnetic beads. In the presence of target miRNA, the EDC reaction was initiated, and EDC substrates were dissociated, continuously releasing reporter strands that were labeled with lanthanides (Tb/Ho/Lu). After magnetic separation, the supernatant containing the released reporter strands was introduced into an ICP-MS system for simultaneous detection of ¹⁵⁹Tb/¹⁶⁵Ho/¹⁷⁵Lu and quantification of miRNA-21, miRNA-155, and miRNA-10b, respectively. The limits of detection were 7.4, 7.5, and 11 pmol L^-1 for miRNA-21, miRNA-155, and miRNA-10b, respectively. Overall, this study provides a powerful strategy for simultaneous quantification of multiple miRNAs, with the advantages of flexible probe design, good sensitivity, and excellent specificity.

Single-Nanoparticle Differential Immunoassay for Multiplexed Gastric Cancer Biomarker Monitoring

Precision medicine demands the best application of multiple unambiguous biomarkers to bring uniform decisions in disease prognosis. The remarkable development of heterogeneous immunoassay greatly promotes precision medicine when combined with the biomarker combination strategy. Nevertheless, the cumbersome washing steps in heterogeneous immunoassay have inevitably compromised the accuracy because of the sample losses and nature change of the matrix, challenging the further exploration of a more facile and lower limit-of-detection analysis. The new methodologies with high throughputs and specificity are never out of date to provide simultaneous evaluations and uniform decisions on multiple analytes through a simple process. Herein, we propose a new wash-free immunoassay, named differential assay, for multiplexed biomarker monitoring. The method is based on counting the number difference of unbound nanoparticle tags before and after immunoreactions from a solid support (i.e., magnetic microsphere) by single-particle inductively coupled plasma mass spectrometry (sp-ICP-MS), discarding the tedious washing steps. We primarily explore the proof-of-concept proposal within two types (sandwich and competitive assay), demonstrating the good feasibility for further facile clinical practice. To provide efficient multiplexed evaluations, we synthesized PtNPs with four diameters and screened the most suitable size for efficient differential immunoassay. The wash-free strategy was successfully utilized in simultaneous serological biomarker (CA724, CA199, and CEA) evaluation, with results in good accordance with those measured by the clinical routine method. Potentially, the proposed differential bioassay can be regarded as a more facile and valuable tool in malignancy prognosis and cancer recurrence monitoring.

Standard-free single magnetic bead evaluation: a stable nanoplatform for prostate disease differentiation

Explicit interpretation of heterogeneity between prostate-specific antigen (PSA) subtypes is essential for prostate cancer differentiation during different disease courses, whereas a universal protocol with uniform criteria is still lacking across the globe. In this work, a standard-free single magnetic bead (SMB) nanoplatform utilizing metal nanoparticles with optimal diameters was proposed for prostate disease differentiation in a 134-donor model. The inaccuracy of detection in absolute quantification was diminished via evaluations of metal intensities on the single magnetic bead. The intrinsic proportion of fPSA in tPSA was successfully evaluated by direct use of the Pt to Au intensity ratio (Pt/Au ratio), exhibiting better differentiation between healthy and unhealthy, benign prostatic hyperplasia (BPH) and cancer individuals compared with solo fPSA or tPSA. We generated thresholds respectively for prostate disease differentiation, envisioning that this standard-free SMB nanoplatform would establish a standardized methodology with uniform criteria worldwide in cancer diagnosis, staging, and postoperative assessments.

Single Molecule-Level Detection via Liposome-Based Signal Amplification Mass Spectrometry Counting Assay

Because of the low atomization and/or ionization efficiencies of many biological macromolecules, the application of mass spectrometry to the direct quantitative detection of low-abundance proteins and nucleic acids remains a significant challenge. Herein, we report mass spectrum tags (MS-tags) based upon gold nanoparticle (AuNP)-templated phosphatidylcholine phospholipid (DSPC) liposomes, which exhibit high and reliable signals via electrospray ionization (ESI). Using these MS-tags, we constructed a liposome signal amplification-based mass spectrometric (LSAMS) "digital" counting assay to enable ultrasensitive detection of target nucleic acids. The LSAMS system consists of liposomes modified with a gold nanoparticle core and surface-anchored photocleavable DNA. In the presence of target nucleic acids, the modified liposome and a magnetic bead simultaneously hybridize with the target nucleic acid. After magnetic separation and photolysis, the MS-tag is released and can be analyzed by ESI-MS. At very low target concentrations, one liposome particle corresponds to one target molecule; thus, the concentration of the target can be estimated by counting the number of liposomes. With this assay, hepatitis C (HCV) virus RNA was successfully analyzed in clinical samples.

Single-Molecule Detection of Nucleic Acids via Liposome Signal Amplification in Mass Spectrometry

A single-molecule detection method was developed for nucleic acids based on mass spectrometry counting single liposome particles. Before the appearance of symptoms, a negligible amount of nucleic acids and biomarkers for the clinical diagnosis of the disease were already present. However, it is difficult to detect extremely low concentrations of nucleic acids using the current methods. Hence, the establishment of an ultra-sensitive nucleic acid detection technique is urgently needed. Herein, magnetic beads were used to capture target nucleic acids, and liposome particles were employed as mass tags for single-particle measurements. Liposomes were released from magnetic beads via photocatalytic cleavage. Hence, one DNA molecule corresponded to one liposome particle, which could be counted using mass spectrometric measurement. The ultrasensitive detection of DNA (10^-18 M) was achieved using this method.

Multiplex DNA Walking Machines for Lung Cancer-Associated miRNAs

Biomimetic DNA walking machines have gained great success in scrutinizing the microscopic world and sensitive biosensing of disease biomarkers. Despite superb achievements, the research on DNA walking machines for simultaneous detection of multiple analytes is still rare, while the design and realization of multiplexing are considered as an important bottleneck. The multiplex detection of biomarkers can not only improve the specificity of bioassays but also avoid the squander of valuable biological specimens. Herein, we reported multiplex three-dimensional (3D) DNA walking machines based on high-resolution inductively coupled plasma mass spectrometry (HR-ICPMS) for lung cancer-associated miRNA detection. In the presence of lung cancer-associated target miRNAs (miR-21, miR-141, and miR-125b), DNA walking machines were stimulated and operated to liberate a large number of lanthanide elements (Tb, Ho, and Tm), and then the signals were collected simultaneously by HR-ICPMS. The recovery test of target miRNAs in human serum and the simultaneous monitoring experiment of three miRNAs in human lung cancer cell line (A549) and normal cell line (HBE) specimens display satisfactory analysis capabilities for complex biological samples. Thanks to the vast potential of lanthanide tags and the modular design, the proposed bioassay might flexibly detect different miRNA combinations with corresponding sets of DNA walking machines to meet the requirements of various tasks.

HOGG1-assisted DNA methylation analysis via a sensitive lanthanide labelling strategy

The assessment of DNA methylation level is an important indicator for the diagnosis and treatment of some diseases. DNA methylation assays are usually based on nucleic acid amplification strategies, which are time-consuming and complicated in operation procedures. Herein, we proposed a sensitive lanthanide-labelled ICP-MS method for DNA methylation analysis that exploited the feature of Human 8-oxoGuanine DNA Glycosylase (hOGG1), which specifically recognizes 8-oxo-G/5mC base pairs to effectively distinguish methylated DNA. A low limit of detection of 84 pM was achieved, and a 0.1% methylation level can be discriminated in the mixture, without any amplification procedure. Compared with commonly used nucleic acid amplification strategies, this proposed method is time-saving and low probability of false positive. Moreover, this work has been successfully validated in human serum samples, the recovery rates is between 96.7% and 105%, and the relative standard deviation (RSD) is in the range of 3.0%-3.5%, indicating that this method has the potential to be applied in clinical and biological samples quantitative analysis.

A homogeneous nucleic acid assay for simultaneous detection of SARS-CoV-2 and influenza A (H3N2) by single-particle inductively coupled plasma mass spectrometry

In recent years, single particle inductively coupled plasma mass spectrometry (SP-ICP-MS) has become a powerful tool for biological quantitative analysis. Homogeneous analysis method requires no separation and washing steps, which is suited for the analysis of highly infectious pathogens, so as to reduce the risk of infection during the operation. SARS-CoV-2 spreads all over the world, and its early infection symptoms are similar to influenza, which brings inconvenience to triage. Therefore, developing novel analytical method for simultaneous detection of multiple viral nucleic acids is essential. Taking the advantages of SP-ICP-MS and homogeneous analysis strategy, a SP-ICP-MS homogeneous nucleic acid assay by using gold nanoparticles (Au NPs) and silver nanoparticles (Ag NPs) probes was established for simultaneous sensitive analysis of SARS-CoV-2 and influenza A (H3N2). In the present of target SARS-CoV-2 or H3N2 nucleic acids, corresponding Au NPs or Ag NPs probes form larger aggregates, resulting in increased pulse signal intensity and reduced pulse signal frequency of the corresponding NPs in SP-ICP-MS measurement. In this assay, the reaction system of Au NPs and Ag NPs probes does not interfere with each other, and there was no separation and washing procedure, which facilitates operation, saves the analysis time, and improves the analysis efficiency. The linear range of this method is 5-1000 pmol L^-1, with low-level limits of quantification of target nucleic acid. The developed SP-ICP-MS simultaneous homogeneous detection method has a good potential for detecting nucleic acid, protein, cell and other biological samples by changing different modification sequences on the NPs probes.

Metal-Tagged CRISPR/Cas12a Bioassay Enables Ultrasensitive and Highly Selective Evaluation of Kanamycin Bioaccumulation in Fish Samples

The abuse of antibiotics in modern life and aquaculture has become a worldwide problem. Trace amounts of antibiotics discharged into natural water are increased in organisms through bioaccumulation and ultimately harm human health. Herein, we report a metal-tagged CRISPR/Cas12a bioassay and apply it to an ultrasensitive and highly selective evaluation of antibiotics bioaccumulation in wild fish samples. We integrated an element-tagging report probe and collateral cleavage activity of CRISPR/Cas12a. With the recognition and capture of target kanamycin by a "locked-activated" system, the activator strand was subsequently released to activate the collateral cleavage activity of Cas12a, followed by the cleavage of free Tm-Rep. After SA-MB capture, the biotin terminal was modified, and the uncleaved probe of Tm-Rep was removed. The acidized supernate containing the element tag fragment could be directly detected with ¹⁶⁹Tm isotope monitoring by inductively coupled plasma mass spectrometry (ICPMS). With CRISPR/Cas12a biosensing and metal isotope detection by ICPMS, ultrasensitive and fast antibiotics analysis was realized with multiplex detection potential. Taking kanamycin as a modal analyte, a limit of detection as low as 4.06 pM was provided in a 30 min detection workflow. Besides, the bioaccumulation effect of kanamycin in a wild fish sample was also evaluated using the proposed strategy. We investigated the geographical distribution with Pseudorasbora parva samples collected in four different locations along a 600 km stretch of the Yangtze River. In addition, the bioaccumulation kinetics of antibiotics was evaluated in serum, muscle, and liver tissues of Pseudorasbora parva with 7 days of continuous feeding in a kanamycin-enriched environment.

Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules

Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.

Element coding based accurate evaluation of CRISPR/Cas9 initial cleavage

As a powerful gene editing tool, the kinetic mechanism of CRISPR/Cas9 has been the focus for its further application. Initial cleavage events as the first domino followed by nuclease end trimming significantly affect the final on-target rate. Here we propose EC-CRISPR, element coding CRISPR, an accurate evaluation platform for initial cleavage that directly characterizes the cleavage efficiency and breaking sites. We benchmarked the influence of 19 single mismatch and 3 multiple mismatch positions of DNA-sgRNA on initial cleavage, as well as various reaction conditions. Results from EC-CRISPR demonstrate that the PAM-distal single mismatch is relatively acceptable compared to the proximal one. And multiple mismatches will not only affect the cleavage efficiency, but also generate more non-site #3 cleavage. Through in-depth research of kinetic behavior, we uncovered an abnormally higher non-#3 proportion at the initial stage of cleavage by using EC-CRISPR. Together, our results provided insights into cleavage efficiency and breaking sites, demonstrating that EC-CRISPR as a novel quantitative platform for initial cleavage enables accurate comparison of efficiencies and specificities among multiple CRISPR/Cas enzymes.

Initial cleavage events as the first domino of CRISPR/Cas9 kinetic behaviors. To accurately evaluate the initial cleavage of Cas9, element coding CRISPR platform-enabled direct characterization of the cleavage efficiency and cleavage sites was proposed.

Multiplex Nucleic Acid Assay of SARS-CoV-2 via a Lanthanide Nanoparticle-Tagging Strategy

Early diagnosis, early isolation, and early treatment are efficient solutions to control the COVID-19 pandemic. To achieve the accurate early diagnosis of SARS-CoV-2, a multiplex detection strategy is required for the cross-validation to solve the problem of "false negative" of the existing gold standard assay. Here, we present a multicomponent nucleic acid assay platform for SARS-CoV-2 detection based on lanthanide nanoparticle (LnNP)-tagging strategy. For targeting SARS-CoV-2's RNA fragments ORF1ab gene, RdRp gene, and E gene, three LnNP probes can be used simultaneously to identify three sites in one sample through elemental mass spectrometry detection with limits of detection of 1.2, 1.3, and 1.3 fmol, respectively. With the multisite cross-validation, we envision that this multiplex and sensitive detection platform may provide an effective strategy for SARS-CoV-2 fast screening with a high accuracy.

ICP-MS and Photothermal Dual-Readout Assay for Ultrasensitive and Point-of-Care Detection of Pancreatic Cancer Exosomes

Pancreatic cancer is known to have a high mortality rate, and its early diagnosis remains challenging due to the occult location of the pancreas. Exosomes derived from pancreatic cancer cells specifically express glypican-1, which may provide a liquid biopsy opportunity for the early diagnosis of pancreatic cancer. Herein, an inductively coupled plasma mass spectrometry (ICP-MS) and photothermal dual-readout platform was proposed for the ultrasensitive and point-of-care analysis of pancreatic cancer exosomes. In our design, exosomes were specifically captured by the sandwich immunoassay, and simultaneously, alkaline phosphatase was introduced in a low-background manner. The alkaline phosphatase triggered the hydrolysis of l-ascorbic acid 2-phosphate to produce ascorbic acid, followed by the etching of Fe₃O₄@MnO₂ nanoflowers. As a result, the Mn²⁺ generated by etching stripped off the Fe₃O₄ and was quantified using ICP-MS. Meanwhile, the reduced Fe₃O₄@MnO₂ was applied for the photothermal assay by oxidizing dopamine with MnO₂. The protocol exhibits a detection limit down to 19.1 particles mL^-1, which is the most sensitive protocol reported so far. To our knowledge, this is the first endeavor for exosome quantification using ICP-MS and photothermal methods. The developed dual-readout platform not only is capable of distinguishing pancreatic cancer patients from healthy people, but also shows excellent discernibility of individual differences at low concentrations of exosomes. This dual-readout assay is a promising platform for the ultrasensitive and point-of-care detection of exosomes in liquid biopsy-based early cancer diagnosis.

Elemental Mass Spectrometry and Fluorescence Dual-Mode Strategy for Ultrasensitive Label-Free Detection of HBV DNA

This work reported a simple and ultrasensitive label-free method for the detection of hepatitis B virus (HBV) DNA by combining hyperbranched rolling circle amplification (HRCA) with dual-mode detection by inductively coupled plasma mass spectrometry (ICP-MS) and fluorescence using ruthenium complex [Ru(bpy)₂dppz]²⁺ (bpy = 2,2'-bipyridine, dppz = dipyrido [3,2-a:2',3'-c] phenazine) as a dual functional probe. An HBV DNA-initiated HRCA system was designed to realize the highly efficient amplification of HBV DNA with the generation of a mass of dsDNA. Also, the [Ru(bpy)₂dppz]²⁺ probe was then added to intercalate into the dsDNA products, resulting in strong fluorescence recovery of the probe for fluorescence detection. Meanwhile, using a biotin-modified primer in HRCA, the dsDNA-[Ru(bpy)₂dppz]²⁺ complexes could be captured by the avidin-coated 96-well plates, and the captured [Ru(bpy)₂dppz]²⁺ probe was later desorbed by acid for ICP-MS detection. The linear range of the proposed method was 3.5-200 amol L^-1 and the limit of detection (LOD) was 1 amol L^-1 for ICP-MS detection, while the linear range was 20-500 amol L^-1 and the LOD was 9.6 amol L^-1 for fluorescence detection. The developed method was applied to human serum sample analysis, and the analytical results coincided very well with those obtained by the real-time polymerase chain reaction (PCR) method. The developed dual-mode label-free detection method was ultrasensitive, simple, and accurate, showing great potential for therapeutic monitoring of HBV infection.

Single-Nanoparticle ICP-MS for Sensitive Detection of Uracil-DNA Glycosylase Activity

Single-nanoparticle inductively coupled plasma mass spectrometry (SP-ICP-MS) has demonstrated unique advantages for the detection of biological samples. However, methods for enzyme activity detection based on SP-ICP-MS technology have been rarely explored. Here we report the development of a novel SP-ICP-MS assay for uracil-DNA glycosylase (UDG) activity detection based on its ability to specifically recognize and remove uracil to induce the cleavage of the DNA probe. Our design allows the generation of single gold nanoparticles correlated to the specific enzymatic reaction for a highly sensitive SP-ICP-MS measurement. The developed assay enables sensitive UDG activity detection with a detection limit of 0.0003 U/mL. The cell lysate analysis by the developed assay reveals its applicability for the detection of UDG activity in real samples. It is envisioned that our design may provide a new paradigm for developing the SP-ICP-MS assay for enzyme activity detection in biological samples.

A multiplex bacterial assay using an element-labeled strategy for 16S rRNA detection

A multiplex bacterial assay method that combines S1 nuclease pretreatment and ICP-MS-based elemental labels is presented in this work. Six intestinal related bacteria were identified at the species level and quantified simultaneously without isolation culturing. This method could be extended to assay a mixed bacterial community for point-of-care diagnosis.

Noble-metal nanoparticle labelling multiplex miRNAs by ICP-MS readout with internal standard isotopes of 115In and 209Bi

Inductively coupled plasma-mass spectrometry (ICP-MS) is one of the most powerful techniques for multiplex nucleotide assay owing to the virtue of the high resolution of multiple-elements' mass to charge ratio, in a mass spectrum. Here, a small sized (less than 20 nm) noble-metal nanoparticle labelled ICP-MS (NP-ICP-MS) is proposed for high-throughput microRNA (miRNA) determination. Three miRNA targets - miR-486-5p, miR-221, and miR-21 - in serum, were distinguished by single-stranded DNA (ssDNA) probes labelled with a small sized noble-metal nanoparticle - silver nanoparticles (AgNPs), platinum nanoparticles (PtNPs), and gold nanoparticles (AuNPs). The counting isotopes ion intensity per second (CPS) of the noble-metal label versus internal standard isotope intensity of ¹¹⁵In and ²⁰⁹Bi, exhibited good linearity in the range 0.25 pM to 100 pM with correlation coefficients (R²) of 0.9680, 0.9305, and 0.9418. The specific sandwich-type miRNA assay using the sensitive NP-ICP-MS readout pushed the detection limits down to 0.18 pM for miR-221, 0.23 pM for miR-486-5p, and 0.22 pM for miR-21. And the relative standard deviations (RSDs) for 10 pM target miRNA were less than 3.7%. This work promises a potential ultrasensitive ICP-MS bioassay of multiplex miRNA biomarkers for clinical serum diagnosis.

Filter-Assisted Separation of Multiple Nanomaterials: Mechanism and Application in Atomic/Mass Spectrometry/Fluorescence Label-Free Multimode Bioassays

Atomic spectrometry (AS) has been widely used in bioassay, but it requires steps to immobilize or separate the signal molecules. In this work, based on the phenomenon that the filter membrane can selectively separate multiple nanomaterials (nanoparticles (NPs) and quantum dots (QDs)) and its related ions, including poly(thymine)-templated Cu NPs and free Cu²⁺, Ag NPs and free Ag⁺, CdTe QDs and Cd²⁺, we constructed multimode and label-free biosensors by chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS), inductively coupled plasma mass spectrometry (ICP-MS), and fluorescence. In this strategy, terminal deoxynucleotidyl transferase (TdT) and polynucleotide kinase (PNK), H₂O₂, and mucin 1 can be sensitively detected using Cu²⁺, Ag⁺, and Cd²⁺ as the signal probe, respectively. As a result, TdT and T4 PNK in single cells level can be accurately quantified. In addition, the possible separation mechanism of filter membrane was proposed, both Donnan repulsion by charged functional layer and entrapment effect by nanomaterials size contributed to the outstanding separation performance. Subsequently, on the basis that CdTe QDs can selectively identify Cu NPs/Cu²⁺, Ag NPs/Ag⁺, and C-Ag⁺-C/Ag⁺, cation-exchange reaction (CER) was introduced in this platform due to its unique advantages, including improving the sensitivity of the above system (an order of magnitude), converting the non-CVG metal elements into CVG elements, and using low-cost AFS to substitute the high-cost ICP-MS. In addition, we performed theoretical calculations of the selective CER using density functional theory (DFT). Therefore, this label-free and simple separation AS/ICP-MS sensing platform shows great potential for biomarker analysis.

A nanoprobe based on molybdenum disulfide nanosheets and silver nanoclusters for imaging and quantification of intracellular adenosine triphosphate

Adenosine triphosphate (ATP), as a high-energy phosphate compound that stores and releases energy in living cells, has an irreplaceable role in many physiological processes and maintenance of biological functions, and can be used as an indicator of many diseases. In this work, a composite nanoprobe, silver nanocluster (AgNC) @ molybdenum disulfide (MoS₂), was designed to achieve in situ fluorescence imaging and quantitative analysis of intracellular ATP in HeLa cells by fluorescence spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). The probe was constructed based on the adsorption of DNA-AgNCs by MoS₂ nanosheets, and the DNA-AgNCs were prepared with the ATP aptamer as a template, whose fluorescence was initially quenched by MoS₂. When the probe was incubated into the cells, intracellular ATP recognized the aptamer sequence and caused the DNA-AgNCs to fall off the MoS₂ nanosheets, resulting in fluorescence recovery. Here, AgNCs not only acted as a fluorescence label for imaging, but also as an element tag for quantitative analysis of intracellular ATP with the detection of ¹⁰⁷Ag by ICP-MS. The ATP in HeLa cells detected by this method was 24.6 ± 1.7 nmol L^-1, which was in good agreement with the test result of the ATP test kit (20.4 ± 0.8 nmol L^-1). The proposed method has potential application in medical clinical diagnosis and evaluation of the body's metabolic level via fluorescence imaging and ICP-MS detection of intracellular ATP.

Tag-Free Methodology for Ultrasensitive Biosensing of miRNA Based on Intrinsic Isotope Detection

MicroRNA (miRNA), of which the abnormal intracellular expression highly associates with numerous pathological diseases, is considered as an important biomarker for early diagnosis and state monitoring of cancer. To avoid the tedious and vunerable labeling process, a series of novel label-free quantification methods for miRNA have been proposed. However, current label-free miRNA assays still require the presynthesis of a sensing unit as tags. Herein, we propose a "tag-free" methodology for miRNA quantification to realize the removal of sensing labels. Combining a concatenated-HCR (C-HCR) strategy and high-resolution inductive couple plasma mass spectrometry (HR-ICPMS) detection, we utilize phosphorus as a characteristic element to quantify the concentration of nucleotides. Benefiting from the excellent amplification performance of C-HCR and element analysis capacity of HR-ICPMS, a 13 fM limit of detection (LOD) was obtained. Ulteriorly, we verify the anti-interference performance of the proposed tag-free miRNA assay with a phosphate substrate-contained cell culture medium or nontarget miRNA. Furthermore, two cell lines of human cancer were chosen to evaluate the real biological sample analysis capacity. The good correlation data indicate promising prospects of the proposed tag-free methodology for the quantification of miRNA in tumor cells and further clinical applications.

Isotopic core-satellites enable accurate and sensitive bioassay of adenosine triphosphate

Adenosine triphosphate is a major vector of chemical energy in living organisms, but its detection is sometimes hindered by complicated physiological sample matrixes. In this work, we demonstrated a ratiometric bioassay for the accurate and sensitive detection of ATP by measuring the ¹⁹⁷Au/¹¹⁵In signal ratio of a mass spectrometric core-satellite structure. Validation of the proposed bioassay was successfully demonstrated in cell lysates and human serum samples.

Sensitive CVG-AFS/ICP-MS label-free nucleic acid and protein assays based on a selective cation exchange reaction and simple filtration separation

Nowadays, label-free atomic spectrometric bioassays are attracting great research interest because of their advantages of low cost, simple design and operation, etc. Herein, a novel and simple chemical vapor generation-atomic fluorescence spectrometry (CVG-AFS)/inductively coupled plasma-mass spectrometry (ICP-MS) label-free detection method is presented for highly sensitive and selective assay of DNA and proteins. This work mainly combined a phenomenon that CdTe quantum dots (QDs) can be used to selectively differentiate free Hg2+ and the T-Hg2+-T complex, with the use of simple membrane filtration separation to improve the performance of the label-free bioassay methods. Upon hybridization with the DNA/protein (carcinoembryonic antigen, CEA) target, the T-Hg2+-T hairpin structure was opened and Hg2+ was released; this initiated the cation exchange reaction between Hg2+ and CdTe QDs which released Cd2+ simultaneously. Subsequently, the free Cd2+ was separated by the filtration membrane without separating the CdTe QDs, which could then be separated from the sample matrices for the CVG-AFS/ICP-MS assay. Under the optimal conditions, this method possessed high sensitivity for DNA and CEA determination with limits of detection (LODs) of 0.2 nM and 0.2 ng mL-1, and linear dynamic ranges of 1-160 nM and 0.5-20 ng mL-1, respectively, and exhibited excellent DNA sequence specificity and protein selectivity. This method preserves the advantages of the label-free atomic spectrometric bioassay, and combined with the selective cation exchange reaction and simple filtration separation to improve the performance.

Nucleic acid and SNP detection via template-directed native chemical ligation and inductively coupled plasma mass spectrometry

Detection of nucleic acids and single nucleotide polymorphisms (SNPs) is of pivotal importance in biology and medicine. Given that the biological effect of SNPs often is enhanced in combination with other SNPs, multiplexed SNP detection is desirable. We show proof of concept of the multiplexed detection of SNPs based on the template-directed native chemical ligation (NCL) of PNA-probes carrying a metal tag allowing detection using ICP-MS. For the detection of ssDNA oligonucleotides (30 bases), two probes, one carrying the metal tag and a second one carrying biotin for purification, are covalently ligated. The methodological limit of detection is of 29 pM with RSD of 6.7% at 50 pM (n = 5). Detection of SNPs is performed with the combination of two sets of reporter probes. The first probe set targets the SNP, and its yield is compared with a second set of probes targeting a neighboring sequence. The assay was used to simultaneously differentiate between alleles of three SNPs at 5-nM concentration.

Simultaneous determination of two phosphorylated p53 proteins in SCC-7 cells by an ICP-MS immunoassay using apoferritin-templated europium(III) and lutetium(III) phosphate nanoparticles as labels

Phosphorylated p53 proteins are biomarkers with clinical utility for early diagnosis of cancer, but difficult to quantify. An inductively coupled plasma mass spectrometry (ICP-MS) based immunoassay is described here that uses uniform lanthanide nanoparticles (NPs) as elemental tags for the simultaneous determination of two phosphorylated p53 proteins. Apoferritin templated europium (Eu) phosphate (AFEP) NPs and apoferritin templated lutetium (Lu) phosphate (AFLP) NPs with 8 nm in diameter were used to label two phosphorylated p53 proteins at serine 15 and serine 392 sites (p-p53¹⁵ and p-p53³⁹²), respectively. The assay has a sandwich format, and p-p53¹⁵ and p-p53³⁹² were first captured and then recognized by AFEP and AFLP NPs labelled antibodies, respectively. The Eu and Lu were then released from the immune complexes under acidic condition for ICP-MS measurement. The limits of detection for p-p53¹⁵ and p-p53³⁹² are 200 and 20 pg·mL^-1, with linear ranges of 0.5-20 and 0.05-20 ng·mL^-1, respectively. The method was further applied to study the response of p-p53¹⁵ and p-p53³⁹² in SCC-7 cells exposed to the natural carcinogen arsenite. A significant up-regulation of p-p53¹⁵ and p-p53³⁹² can be observed when cells were exposed to arsenite at 5 μmol·L^-1 level for 24 h. Graphical abstract Schematic presentation of the ICP-MS immunoassay using apoferritin templated europium (III) and lutetium (III) phosphate nanoparticles as labels for the simultaneous determination of two phosphorylated p53 proteins. Europium (Eu) phosphate nanoparticles (blue) and lutetium (Lu) phosphate nanoparticles (pink) were synthesized in the size-restricted cavity of apoferritin. They were further coupled with antibodies to prepare Eu and Lu labelled probes for p-p53¹⁵ (blue) and p-p53³⁹² (pink), respectively. After formation of a a sandwich, the labelled Eu and Lu were dissociated in acid and then introduced to ICP-MS for the simultaneous determination of two phosphorylated p53 proteins p-p53¹⁵ (blue) and p-p53³⁹² (pink).

Molecules and elements for quantitative bioanalysis: The allure of using electrospray, MALDI, and ICP mass spectrometry side-by-side

To understand biological processes, not only reliable identification, but quantification of constituents in biological processes play a pivotal role. This is especially true for the proteome: protein quantification must follow protein identification, since sometimes minute changes in abundance tell the real tale. To obtain quantitative data, many sophisticated strategies using electrospray and MALDI mass spectrometry (MS) have been developed in recent years. All of them have advantages and limitations. Several years ago, we started to work on strategies, which are principally capable to overcome some of these limits. The fundamental idea is to use elemental signals as a measure for quantities. We began by replacing the radioactive ³² P with the "cold" natural ³¹ P to quantify modified nucleotides and phosphorylated peptides and proteins and later used tagging strategies for quantification of proteins more generally. To do this, we introduced Inductively Coupled Plasma Mass Spectrometry (ICP-MS) into the bioanalytical workflows, allowing not only reliable and sensitive detection but also quantification based on isotope dilution absolute measurements using poly-isotopic elements. The detection capability of ICP-MS becomes particularly attractive with heavy metals. The covalently bound proteins tags developed in our group are based on the well-known DOTA chelate complex (1,4,7,10-tetraazacyclododecane-N,N',N″,N‴-tetraacetic acid) carrying ions of lanthanoides as metal core. In this review, I will outline the development of this mutual assistance between molecular and elemental mass spectrometry and discuss the scope and limitations particularly of peptide and protein quantification. The lanthanoide tags provide low detection limits, but offer multiplexing capabilities due to the number of very similar lanthanoides and their isotopes. With isotope dilution comes previously unknown accuracy. Separation techniques such as electrophoresis and HPLC were used and just slightly adapted workflows, already in use for quantification in bioanalysis. Imaging mass spectrometry (MSI) with MALDI and laser ablation ICP-MS complemented the range of application in recent years.

Enzyme-free amplified DNA assay: five orders of linearity provided by metal stable isotope detection

For the quantification of mutated genes at greatly varied concentrations in body fluids, nucleic acid amplification strategies are often challenged by limited dynamic linear ranges. The proposed metal stable isotope detection strategy demonstrates five orders of linear range and a lower attomol detection limit, showing promising potential in clinical diagnosis.

Poly(thymine)-CuNPs: Bimodal Methodology for Accurate and Selective Detection of TNT at Sub-PPT Levels

Accurate, sensitive, and selective detection of explosives is of vital importance in antiterrorism and homeland security. Fluorescence sensors are prevalent for sensitive and fast in-field explosive detection but are sometimes compromised by accuracy and stability due to the similar structures of explosives, photobleaching, and complex sample matrixes. Herein, we developed a first bimodal methodology capable of both sensitive in-field fluorescence detection and accurate laboratory mass spectrometric quantification of 2,4,6-trinitrotoluene (TNT) by utilizing the characteristic fluorescent and mass spectrometric response of copper nanoparticles (CuNPs). An excellent selectivity was also realized by involving aptamer recognition. The methodology is capable of detecting TNT at subpart per trillion (PPT) levels, with a detection limit of 0.32 pg mL^-1 by inductively coupled plasma mass spectrometry (ICPMS) and 0.17 ng mL^-1 by fluorimetry. The signal response was accurate and stable for at least 60 days by ICPMS. Thanks to the biospecificity of the aptamer, this bimodal methodology is potentially applicable to a large panel of explosives.

Ratiometric quantification of β2-microglobulin antigen in human serum based on elemental labeling strategy

Ratiometric quantification for competitive immunoassay based on internal standard element detection utilizing inductively coupled plasma mass spectrometry (ICP-MS) as multiplex readout has been demonstrated. The Beta-2-microglobulin (β2-MG) associated with clinical diseases was detected by Y-labeled capture antibody used as internal standard probes and Sm-labeled antigen used as report probes via antigen-antibody reaction. The ratiometric quantification was achieved by taking the signal ratio of Sm/Y. The ratiometric method could compensate for the particle loss and suppress the signal fluctuation, which improved the precision of the quantitative result. Under the optimized conditions, the calibration curves for β2-MG antigen was linear in the range of 0.25-8.0 μg/mL with a detection limit of 0.17 μg/mL (3σ, n = 11). The recoveries of 96.5%-132% were obtained for serum samples spiked with different concentration standards, and the relative standard deviation (RSD) was less than 10%. The β2-MG results in serum samples obtained by the proposed method correlated well with those obtained by time-resolved fluorescence immunoassay (r = 0.947). This proposed method provides a simpler labeling strategy for ratiometric quantification of immunoassay.