Proline: an efficient and user-friendly software suite for large-scale proteomics.

MOTIVATION: The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. RESULTS: Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline's ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. AVAILABILITY AND IMPLEMENTATION: Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client-server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Oxidative stress is decreased in physically active sickle cell SAD mice.

Oxidative stress plays a crucial role in sickle cell disease (SCD) physiopathology. Given that chronic physical activity is known to decrease reactive oxygen species (ROS) and increase nitric oxide (NO) bioavailability in healthy subjects and in patients with cardiovascular or inflammatory pathologies, modulating these factors involved in the severity of the pathology could also be beneficial in SCD. This study aimed to determine if 8 weeks of increased physical activity (PA) by voluntary wheel running affects the hypoxia/reoxygenation (H/R) responses by reducing oxidative stress and increasing NO synthesis in sickle SAD mice. Nitrite/nitrate (NOx) concentrations, NOS3 mRNA expression and phosphorylated-endothelial nitric oxide synthase immunostaining were increased in the lungs of the PA groups after H/R stress. Moreover, lipid peroxidation in the heart was decreased in PA SAD mice. The improvement of antioxidant activity at rest and the decrease in haemolysis may explain this reduced oxidative stress. These results suggest that physical activity probably diminishes some deleterious effects of H/R stress in SAD mice and could be protective against vascular occlusions.