Quantitative protein detection using single molecule imaging enzyme-linked immunosorbent assay (iELISA)

Proteomes Are of Proteoforms: Embracing the Complexity

Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?

Calibration-Free Single-Molecule Absolute Quantification Using Super-resolution Microscopy

Single-molecule (SM) quantification has become a powerful analytical technique in the fields of physics, chemistry, and biology. SM imaging, especially with super-resolution (SR) techniques, has dramatically facilitated the study of individual molecules that may function as disease-related biomarkers. Although multiple properties can be used for quantitative imaging analysis, counting may be the simplest and most direct way. Consequently, how to utilize the greater spatial resolution to overcome undercounting or overcounting errors in certain conditions shows promising potential to unravel intracellular mechanisms of isolated biomolecules. From this perspective, we present an absolute quantification approach, termed crucial connected-component entropy (CCCE), with subresolution accuracy for the SR SM detection platform without the need for prior knowledge of calibration, and a cross-validation analytical pipeline based on SM profiling for nanoscale performance assessments. Considering its high efficiency, accuracy, and robustness for routine SM quantification compared with commonly used strategies, we believe that this protocol will indubitably find wide applications in biochemistry research, drug discovery, and clinical diagnostics, especially molecular diagnostics.

Sensitive antibody fluorescence immunosorbent assay (SAFIA) for rapid on-site detection on avian influenza virus H9N2 antibody

Avian influenza virus (AIV) is a serious zoonotic disease causing severe damages to both poultry industry and human health. To rapidly detect AIV on-site with high sensitivity and accuracy, we design sensitive antibody fluorescence immunosorbent assay (SAFIA) on AIV H9N2 antibody. In SAFIA, hemagglutinin (HA1) protein coated sample chamber specifically binds targets but remarkably reduces non-specific absorption; Protein L coated polystyrene microsphere captures target through secondary antibody to significantly amplify the fluorescence signal; and a portable fluorescence counter automatically measures the fluorescence spot density for AIV H9N2 antibody detection. Proved by practical applications, SAFIA could probe AIV H9N2 antibody in high sensitivity and selectivity, and distinguish positive and negative serum samples in high accuracy. Additionally, SAFIA can rapidly detect AIV H9N2 antibody at room temperature only requiring simple operations as well as cost-effective and compact devices. Therefore, SAFIA is a potential new-generation tool in rapid on-site testing for agricultures.

Cysteine specific bioconjugation with benzyl isothiocyanates

Protein labelling has a wide variety of applications in medicinal chemistry and chemical biology. In addition to covalent inhibition, specific labelling of biomolecules with fluorescent dyes is important in both target discovery, validation and diagnostics. Our research was conducted through the fragment-based development of a new benzyl-isothiocyanate-activated fluorescent dye based on the fluorescein scaffold. This molecule was evaluated against fluorescein isothiocyanate, a prevalent labelling agent. The reactivity and selectivity of phenyl- and benzyl isothiocyanate were compared at different pHs, and their activity was tested on several protein targets. Finally, the clinically approved antibody trastuzumab (and it's Fab fragment) were specifically labelled through reaction with free cysteines reductively liberated from their interchain disulfide bonds. The newly developed benzyl-fluorescein isothiocyanate and its optimized labelling protocol stands to be a valuable addition to the tool kit of chemical biology.

We present herein the development of a new fluorescent dye equipped with a benzyl isothiocyanate warhead, which resulted improved photophysical properties and enhanced labelling efficiency on the Fab antibody subunit and the trastuzumab antibody.