Search

Selective enrichment of specific peptides is an effective way to identify low abundance proteins. Fractionation of peptides prior to mass spectrometry is another widely used approach to reduce sample complexity in order to improve proteome coverage.In this study, we designed a multi-stage digestion strategy to generate peptides with different trypsin cleavage kinetics. It was found that each of the collected peptide fractions yielded many new protein identifications compared to the control group due to the reduced complexity. The overlapping peptides identified between adjacent fractions were very low, indicating that each fraction had different sets of peptides. The multi-stage digestion strategy separates tryptic peptides with different cleavage kinetics while RPLC separates peptides with different hydrophobicity. These two separation strategies were highly orthogonal, and showed an effective multidimensional separation to improve proteome coverage., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A simple, cost-effective and high throughput method was developed for multiplexed kinase activity assay based on the multiplex isotope labeling of designed substrate peptides. This strategy was successfully applied to monitor the time-dependent consumption of substrates and generation of products in the single and multiple substrate systems.

Because of the health benefits and economic opportunities, extracting bioactive peptides from plant proteins, often food processing by-products, garners significant interest. However, the high enzyme costs and the emergence of bitter peptides have posed significant challenges in production. This study achieved the immobilization of Alcalase and Flavorzyme using cost-effective SiO2 microparticles. Mussel-inspired chemistry and biocompatible polymers were employed, with genipin replacing glutaraldehyde for safer crosslinking. This approach yielded an enzyme loading capacity of approximately 25 mg/g support, with specific activity levels reaching around 180 U/mg for immobilized Alcalase (IA) and 35 U/mg for immobilized Flavorzyme (IF). These immobilized proteases exhibited improved activity and stability across a broader pH and temperature range. During the hydrolysis of soy proteins, the use of immobilized proteases avoided the thermal inactivation step, resulting in fewer peptide aggregates. Moreover, this study applied peptidomics and bioinformatics to profile peptides in each hydrolysate and identify bioactive ones. Cascade hydrolysis with IA and IF reduced the presence of bitter peptides by approximately 20%. Additionally, 50% of the identified peptides were predicted to have bioactive properties after in silico digestion simulation. This work offers a cost-effective way of generating bioactive peptides from soy proteins with reducing potential bitterness. [ABSTRACT FROM AUTHOR]

Stable isotope dimethyl labeling, a widely used method for quantitative proteomics, was extended to five channels for the first time. Comprehensive proteome and phosphoproteome quantification validated the high quantification accuracy and throughput of this five-plex method. [ABSTRACT FROM AUTHOR]