We have received feedback from our users and supporters on the functionality and usability of the Swiss Grid Proteomics Portal during its first year of operation. We have also realized which aspects of the portal could be improved upon through frequent monitoring and interaction with the production system under heavy use. In a second, highly upgraded version of the Swiss Proteomics Portal, call...

Sperm proteomics is the identification and functional study of sperm proteins. It is based on the separation of proteins to generate a sample suitable for mass spectrometry and subsequent protein identification. Various proteomic approaches can be employed to study sperm proteins. Currently it has led to the identification and cataloging of thousands of sperm proteins. Ultimately, the goal is t...

glaucoma, a group of multifactor ocular diseases, is the second leading cause of blindness worldwide. primary open angle (poa) is the most common type of glaucoma, characterized by progressive optic nerve degeneration. numerous genes and proteins have been revealed to be associated with poag, but the pathologic mechanisms of the disease are still poorly understood. proteomics, the collective st...

Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique prot...

Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology...

The analysis by liquid chromatography coupled to tandem mass spectrometry of complex peptide mixtures, generated by proteolysis of protein samples, is the main proteomics method used today. The approach is based on the assumption that each protein present in a sample reproducibly and predictably generates a relatively small number of peptides that can be identified by mass spectrometry. In this...

A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to p...

Stable isotope coding continues to be a powerful approach in comparative proteomics. This review focuses on recent developments in stable isotope coding-based strategies targeted towards protein expression, protein interactions with other biomolecules, post-translational modifications and absolute quantification. The focus of the bulk of proteomics studies is still on protein expression. An imp...

With the advent of robust and high-throughput mass spectrometric technologies bioinformatics tools to analyze large data sets, proteomics has penetrated broadly into basic translational life sciences research. More than 95% FDA-approved drugs currently target proteins, most diagnostic tests are protein-based. The introduction clinic, for instance guide patient stratification treatment, i...

The last decade has witnessed remarkable technological advances in mass spectrometry-based proteomics. The development of proteomics techniques has enabled the reliable analysis of complex proteomes, leading to the identification and quantification of thousands of proteins in gastric cancer cells, tissues, and sera. This quantitative information has been used to profile the anomalies in gastric...