New Structure Mass Tag based on Zr-NMOF for Multiparameter and Sensitive Single-Cell Interrogating in Mass Cytometry

Integrating aptasensor with an explosive mass-tag signal amplification strategy for ultrasensitive and multiplexed analysis using a miniature mass spectrometer

Mass probes attached with aptamers and mass tags offer excellent specificity and sensitivity for multiplexed detection, wherein the dissociation of mass tags from the mass probes is as important as their labeling. Herein, aggregation-induced emission luminogen (AIEgen)-tagged mass probes (AIEMPs) were established to analyze estrogens, which integrated aptasensor with an explosive mass-tag signal amplification strategy via a simple ultrasound-assisted emulsification of nanoliposomes. The AIEMPs were assembled by the hybridization of aptamer-modified Fe3O4 nanoparticles (Fe NPs@Apt) and nanoliposomes loaded with massive AIEgen mass tags and partially complementary DNA strands (AIE NLs@cDNA). The aptamer was preferentially and specifically bound to estrogen, resulting in the detachment of AIE NLs from AIEMPs. Subsequently, the AIEMPs were deposited with electrospray solvents for explosive release of mass tags. Using nanoelectrospray ionization mass spectrometry (nanoESI-MS), the AIEMP-based aptasensor achieved ultrasensitive analysis of estrogens with limits of detection of 0.168-0.543 pg/mL and accuracies in the range of 87.9-114.0%. Compared to direct nanoESI-MS detection, the AIEMP-based aptasensor provides a signal amplification of four orders of magnitude. Furthermore, the utilization of different AIEMPs enables multiplexed detection of three estrogens with a miniature mass spectrometer, showing promising potential for on-site detection. This work expands the diversity of mass-tagging strategy and provides a versatile mass probe-based aptasensor platform for routine MS detection of trace analytes.

Advancing Breast Cancer Heterogeneity Analysis: Insights from Genomics, Transcriptomics and Proteomics at Bulk and Single-Cell Levels

Breast cancer continues to pose a significant healthcare challenge worldwide for its inherent molecular heterogeneity. This review offers an in-depth assessment of the molecular profiling undertaken to understand this heterogeneity, focusing on multi-omics strategies applied both in traditional bulk and single-cell levels. Genomic investigations have profoundly informed our comprehension of breast cancer, enabling its categorization into six intrinsic molecular subtypes. Beyond genomics, transcriptomics has rendered deeper insights into the gene expression landscape of breast cancer cells. It has also facilitated the formulation of more precise predictive and prognostic models, thereby enriching the field of personalized medicine in breast cancer. The comparison between traditional and single-cell transcriptomics has identified unique gene expression patterns and facilitated the understanding of cell-to-cell variability. Proteomics provides further insights into breast cancer subtypes by illuminating intricate protein expression patterns and their post-translational modifications. The adoption of single-cell proteomics has been instrumental in this regard, revealing the complex dynamics of protein regulation and interaction. Despite these advancements, this review underscores the need for a holistic integration of multiple 'omics' strategies to fully decipher breast cancer heterogeneity. Such integration not only ensures a comprehensive understanding of breast cancer's molecular complexities, but also promotes the development of personalized treatment strategies.

A universal mass tag based on polystyrene nanoparticles for single-cell multiplexing with mass cytometry

Mass cytometry (MC) is an emerging bioanalytical technique for high-dimensional biomarkers interrogation simultaneously on individual cells. However, the sensitivity and multiplexed analysis ability of MC was highly restricted by the current metal chelating polymer (MCP) mass tags. Herein, a new design strategy for MC mass tags by using a commercial available and low cost classical material, polystyrene nanoparticle (PS-NP) to carry metals was reported. Unlike inorganic materials, sub-micron-grade metal-loaded polystyrene can be easily detected by MC, thus it is not essential to pursue extremely small particle size in this mass tag design strategy. An altered cell staining buffer can significantly lower the nonspecific binding (NSB) of non-functionalized PS-NPs, revealing another method to lower NSB beside surface modification. The metal doped PS-NP_Abs mass tags showed high compatibility with MCP mass tags and 5-fold higher sensitivity. By using Hf doped PS-NP_Abs as mass tags, four new MC detection channels (¹⁷⁷Hf, ¹⁷⁸Hf, ¹⁷⁹Hf and ¹⁸⁰Hf) were developed. In general, this work provides a new strategy in designing MC mass tags and lowering NSB, opening up possibility of introducing more potential MC mass tag candidates.

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.

Reagents for Mass Cytometry

Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm² spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.

Sickle-like Inertial Microfluidic System for Online Rare Cell Separation and Tandem Label-Free Quantitative Proteomics (Orcs-Proteomics)

Label-free proteomics with trace clinical samples provides a wealth of actionable insights for personalized medicine. Clinically acquired primary cells, such as circulating tumor cells (CTCs), are usually with low abundance that is prohibitive for conventional label-free proteomics analysis. Here, we present a sickle-like inertial microfluidic system for online rare cell separation and tandem label-free proteomics (namely, Orcs-proteomics). Orcs-proteomics adopts a buffer system with 0.1% N-dodecyl β-d-maltoside (DDM), 1 mM Tris (2-carboxyethyl) phosphine (TCEP), and 2 mM 2-chloroacetamide (CAA) for cell lysis and reductive alkylation. We demonstrate the application of Orcs-proteomics with 293T cells and manage to identify 913, 1563, 2271, and 2770 protein groups with 4, 13, 68, and 119 cells, respectively. We then spike MCF7 cells with white blood cells (WBCs) to simulate the patient's blood sample. Orcs-proteomics identifies more than 2000 protein groups with an average of 61 MCF7 cells. We further recruit two advanced breast cancer patients and collect 5 and 7 CTCs from each patient through minimally invasive blood drawing. Orcs-proteomics manages to identify 973 and 1135 protein groups for each patient. Therefore, Orcs-proteomics empowers rare cells simultaneously to be separated and counted for proteomics and provides technical support for personalized treatment decision making with rare primary patient samples.

Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications

Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.

Polymeric dipicolylamine based mass tags for mass cytometry

Mass cytometry is an emerging powerful bioanalytical technique for high-dimensional single-cell analysis. In this technique, cells are stained with metal-isotope-tagged antibodies and are analyzed by an inductively coupled plasma time-of-flight mass spectrometer. While there are more than 100 stable isotopes available in the m/z 75 to 209 detection range of the instrument, only about 50 parameters can be measured per cell because current reagents are metal-chelating polymers with pendant aminocarboxylate chelators that only bind hard metal ions such as the rare earths and Bi³⁺. Here we describe the synthesis and characterization of a new type of metal-chelating polymer with pendant dipicolylamine chelators suited to binding intermediate to soft metals such as rhenium and platinum. We introduce two different conjugation strategies, a thiol–maleimide reaction that works well for rhenium, and a DBCO-azide click reaction designed to avoid potential complications of Pt and other heavy metals interacting with thiol groups. We show that these polymers can serve as new elemental mass tags for mass cytometry. Antibody-polymer conjugates of CD20 and CD8a prepared by both coupling reactions were employed in conjunction with commercial metal-conjugated antibodies for multi-parameter single-cell immunoassays.

A new type of metal-chelating polymer with pendant dipicolylamine chelators that bind rhenium and platinum has been developed for mass cytometry applications.