Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects

MUC1 as a diagnostic biomarker and siRNA-based therapeutic target in breast cancer: A clinical chemistry perspective

Breast cancer remains the leading cause of cancer mortality in women, and early detection coupled with real-time monitoring of tumor burden are clinical imperatives; yet existing imaging-based screening (e.g., mammography, ultrasound) suffers from sensitivities as low as 60-80% and even lower in dense breasts plus substantial false-positive rates, underscoring the critical need for molecular assays with higher accuracy. Current clinical assays for circulating MUC1 (CA15-3) achieve high specificity but exhibit limited sensitivity in early-stage disease, underscoring a critical unmet need for more sensitive, multiplexed biomarkers to enable timely intervention. Mass spectrometry-based glycoproteomic workflows offer multiplexed quantification of tumour-associated MUC1 glycoforms, substantially improving analytical specificity and dynamic range. Complementary liquid-biopsy platforms that detect anti-MUC1 autoantibodies further extend lead time for recurrence detection. Concurrently, small interfering RNA (siRNA) therapies targeting MUC1 delivered via ionizable lipid nanoparticles demonstrate efficient tumor accumulation, robust mRNA knockdown, and favourable safety in phaseI solid tumor trials. In this review, we critically assess the analytical performance and standardization challenges of current MUC1 assays, evaluate emerging mass spectrometry and immunoarray techniques, and examine chemical and nanocarrier strategies that surmount biological barriers to siRNA delivery. We propose a co-development framework for harmonized companion diagnostics and MUC1-directed RNAi therapeutics under unified regulatory pathways, paving the way for precision, biomarker-driven interventions in breast cancer care.

Mass spectrometry analysis of phosphotyrosine-containing proteins

Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.

Determination of adulteration, geographical origins, and species of food by mass spectrometry

Food adulteration, mislabeling, and fraud, are rising global issues. Therefore, a number of precise and reliable analytical instruments and approaches have been proposed to ensure the authenticity and accurate labeling of food and food products by confirming that the constituents of foodstuffs are of the kind and quality claimed by the seller and manufacturer. Traditional techniques (e.g., genomics-based methods) are still in use; however, emerging approaches like mass spectrometry (MS)-based technologies are being actively developed to supplement or supersede current methods for authentication of a variety of food commodities and products. This review provides a critical assessment of recent advances in food authentication, including MS-based metabolomics, proteomics and other approaches.