S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data.

BACKGROUND AND OBJECTIVE: 2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. METHODS: S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. RESULTS: S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. CONCLUSIONS: S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis.

Molecular Plasticity under Ocean Warming: Proteomics and Fitness Data Provides Clues for a Better Understanding of the Thermal Tolerance in Fish.

Ocean warming is known to alter the performance and fitness of marine organisms albeit the proteome underpinnings of species thermal tolerance are still largely unknown. In this 1-month experiment we assessed the vulnerability of the gilt-head sea bream Sparus aurata, taken here as a biological model for some key fisheries species, to ocean warming (control 18°C, nursery ground temperature 24°C and heat wave 30°C). Survival was impaired after 28 days, mainly at 30°C although fishes' condition was unaltered. Muscle proteome modulation was assessed at 14 and 21 days, showing that protein expression profiles were similar between fish exposed to 18 and 24°C, differing from fish exposed to 30°C. Fish subjected to 24°C showed an enhanced glycolytic potential and decreased glycogenolysis mainly at 14 days of exposure. Fish subjected to 30°C also showed enhanced glycolytic potential and up-regulated proteins related to gene expression, cellular stress response (CSR), and homeostasis (mostly cytoskeletal dynamics, acid-base balance, chaperoning). However, inflammatory processes were elicited at 21 days along with a down-regulation of the tricarboxylic acid cycle. Thus, juvenile fish seem able to acclimate to 24°C but possibly not to 30°C, which is the predicted temperature for estuaries during heat waves by the year 2100. This may be related with increasing constraints on organism physiology associated with metabolic scope available for performance and fitness at higher temperatures. Consequently, recruitment of commercial sea breams may be in jeopardy, highlighting the need for improved management plans for fish stocks.

Proteomics analysis of the peritoneal dialysate effluent reveals the presence of calcium-regulation proteins and acute inflammatory response.

BACKGROUND: Peritoneal dialysis (PD) is a form of renal replacement used for advanced chronic kidney disease. PD effluent holds a great potential for biomarker discovery for diagnosis and prognosis. In this study a novel approach to unravelling the proteome of PD effluent based-on dithiothreitol depletion followed by 2D-SDS-PAGE and protein identification using tandem mass spectrometry is proposed. RESULTS: A total of 49 spots were analysed revealing 25 proteins differentially expressed, among them many proteins involved in calcium regulation. CONCLUSIONS: Remarkably, a group of proteins dealing with calcium metabolism and calcium regulation has been found to be lost through peritoneal dialysate effluent, giving thus a potential explanation to the calcification of soft tissues in patients subjected to peritoneal dialysis and kidney injury. Comparison of literature dealing with PD is difficult due to differences in sample treatment and analytical methodologies.