PIPI2: Sensitive Tag-Based Database Search to Identify Peptides with Multiple Post-translational Modifications.

Peptide identification is important in bottom-up proteomics. Post-translational modifications (PTMs) are crucial in regulating cellular activities. Many database search methods have been developed to identify peptides with PTMs and characterize the PTM patterns. However, the PTMs on peptides hinder the peptide identification rate and the PTM characterization precision, especially for peptides with multiple PTMs. To address this issue, we present a sensitive open search engine, PIPI2, with much better performance on peptides with multiple PTMs than other methods. With a greedy approach, we simplify the PTM characterization problem into a linear one, which enables characterizing multiple PTMs on one peptide. On the simulation data sets with up to four PTMs per peptide, PIPI2 identified over 90% of the spectra, at least 56% more than five other competitors. PIPI2 also characterized these PTM patterns with the highest precision of 77%, demonstrating a significant advantage in handling peptides with multiple PTMs. In the real applications, PIPI2 identified 30% to 88% more peptides with PTMs than its competitors.

Phosphoprotein Detection in Sweat Realized by Intercalation Structure 2D@3D g-C3N4@Fe3O4 Wearable Sensitive Motif.

Abnormal protein phosphorylation in sweat metabolites is closely related to cancer, cardiovascular disease, and other diseases. The real-time monitoring of phosphoproteins in sweat is significant for early monitoring of disease biomarkers. Here, a high-efficiency electrochemical sensor for phosphoprotein in sweat was realized by 2D@3D g-C3N4@Fe3O4 with intercalation structure. Common phosphoprotein ß-Casein was selected to demonstrate the platform's functionalities. The detection limit of g-C3N4@Fe3O4 could be as low as 9.7 µM, and the detection range was from 0.01 mg/mL to 1 mg/mL. In addition, the sensing platform showed good selectivity, reproducibility, and stability. We also investigated the effects of interface structure on adsorption properties and electronic properties of the g-C3N4 and Fe3O4 heterostructure using DFT. More electrons from Fe3O4 were transferred to g-C3N4, which increased the electrons in the energy band of N atoms and promoted the formation of stable N-H bonds with H atoms in phosphoproteins. We demonstrated phosphoprotein sensor functionality by measuring the phosphoprotein in human sweat during exercising. This work realizes a sensing platform for noninvasive and continuous detection of sweat phosphoproteins in wearable devices.