Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification.

Mass spectrometry coupled to liquid chromatography is one of the most powerful technologies for proteome quantification in biomedical samples. In peptide-centric workflows, protein mixtures are enzymatically digested to peptides prior their analysis. However, proteome-wide quantification studies rarely identify all potential peptides for any given protein, and targeted proteomics experiments focus on a set of peptides for the proteins of interest. Consequently, proteomics relies on the use of a limited subset of all possible peptides as proxies for protein quantitation. In this work, we evaluated the stability of the human proteotypic peptides during 21 days and trained a deep learning model to predict peptide stability directly from tryptic sequences, which together constitute a resource of broad interest to prioritize and select peptides in proteome quantification experiments.

QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories.

QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated quality control for proteomics experiments in many laboratories. QCloud provides a quick and effortless evaluation of instrument performance that helps to overcome many analytical challenges derived from clinical and translational research. Here we present an improved version of the system, QCloud2. This new version includes enhancements in the scalability and reproducibility of the quality-control pipelines, and it features an improved front end for data visualization, user management, and chart annotation. The QCloud2 system also includes programmatic access and a standalone local version.

Propranolol induces regression of hemangioma cells through HIF-1α-mediated inhibition of VEGF-A.

OBJECTIVE: To investigate the mechanism of propranolol on regression of infantile hemangiomas. BACKGROUND: Propranolol has been found to be effective in treatment of severe hemangiomas of infancy. However, its mechanism of action is as yet unknown. METHODS: Cultured proliferating and involuting hemangioma endothelial cells were treated with varying concentrations of propranolol for up to 4 days. Analysis was performed using cell viability, migration, and tubulogenesis assays, as well as quantitative RT-PCR and flow cytometry. Western blots and ELISA assays were used to assess protein expression. RESULTS: Treatment with propranolol led to a dose dependent cytotoxic effect in hemangioma endothelial cells with decreased cell viability, migration, and tubulogenesis. This cytotoxic effect was VEGF (vascular endothelial growth factor) dependent, as demonstrated by decreased VEGF, VEGF-R1, and VEGF-R2 production. Decreased signaling through the VEGF pathway resulted in downregulation of PI3/Akt and p38/MAPK activity. Decreased VEGF activity was mediated through the hypoxia inducible factor (HIF)-1α pathway but not through NF-κß signaling. CONCLUSIONS: Collectively, these data suggest that propranolol exerts its suppressive effects on hemangiomas through the HIF-1α-VEGF-A angiogenesis axis, with effects mediated through the PI3/Akt and p38/MAPK pathways. These findings provide a plausible mechanism of action of propranolol on regression of infantile hemangiomas.