BRAF protein immunoprecipitation, elution, and digestion from cell extract using a microfluidic mixer for mutant BRAF protein quantification by mass spectrometry

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.

Mass spectrometry-based targeted proteomics for analysis of protein mutations

Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.

Versatile Microfluidic Mixing Platform for High- and Low-Viscosity Liquids via Acoustic and Chemical Microbubbles

Microfluidic mixers have been extensively studied due to their wide application in various fields, including clinical diagnosis and chemical research. In this paper, we demonstrate a mixing platform that can be used for low- and high-viscosity liquid mixing by integrating passive (utilizing the special circulating crossflow characteristics of a zigzag microstructure and cavitation surfaces at the zigzag corners) and active (adding an acoustic field to produce oscillating microbubbles) mixing methods. By exploring the relationship between the active and passive mixing methods, it was found that the microbubbles were more likely generated at the corners of the zigzag microchannel and achieved the best mixing efficiency with the acoustically generated microbubbles (compared with the straight channel). In addition, a higher mixing effect was achieved when the microchannel corner angle and frequency were 60° and 75 kHz, respectively. Meanwhile, the device also achieved an excellent mixing effect for high-viscosity fluids, such as glycerol (its viscosity was approximately 1000 times that of deionized (DI) water at 25 °C). The mixing time was less than 1 s, and the mixing efficiency was 0.95 in the experiment. Furthermore, a new microbubble generation method was demonstrated based on chemical reactions. A higher mixing efficiency (0.97) was achieved by combining the chemical and acoustic microbubble methods, which provides a new direction for future applications and is suitable for the needs of lab-on-a-chip (LOC) systems and point-of-care testing (POCT).