Background In order to tackle the important and challenging problem in proteomics of identifying known and new protein sequences using highthroughput methods, we propose a data-sharing platform that uses fully distributed P2P technologies to share specifications of peer-interaction protocols and service components. By using such a platform, information to be searched is no longer centralised in...

The recent dramatic improvements in high-resolution mass spectrometry (MS) have revolutionized the speed and scope of proteomic studies. Conventional MS-based proteomics methodologies allow global protein profiling based on expression levels. Although these techniques are promising, there are numerous biological activities yet to be unveiled, such as the dynamic regulation of enzyme activity. C...

The possibility of using gene expression profiling by microarrays for purposes of diagnostics, prognostics, and understanding the mechanisms of diseases has also generated much excitement in the past decade. Similarly, mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes (Cox and Mann, 2007). It can be applied to better...

In the life sciences, a new paradigm is emerging that places networks of interacting molecules between genotype and phenotype. These networks are dynamically modulated by a multitude of factors, and the properties emerging from the network as a whole determine observable phenotypes. This paradigm is usually referred to as systems biology, network biology, or integrative biology. Mass spectromet...

UNLABELLED Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library 'mspire'-developed in the Ruby programming language-offers quick and memory-efficient readers for standard xml proteomics formats, converters for in...

Proteomics is the large-scale study of an organism's complete complement of proteins, and its relevant technologies have matured over recent years. Along with the development of mass spectrometry (MS), MS-based proteomics has emerged as an invaluable tool for largescale identification and quantification of protein networks (Aebersold & Mann, 2003; Domon & Aebersold, 2006). Proteomic data is imp...

High-throughput multiplexed proteomics of small-volume biospecimens will generate new opportunities in theranostics. Achieving parallel top-down and bottom-up mass spectrometry analyses of target proteins using a unified apparatus will improve proteome characterization. We have developed a novel silicon-based microfluidic device, multinozzle emitter array chip (MEA chip), as a new platform for ...

The field of proteomics holds great promise for identifying nontargeted, global molecular profiles “signatures” of normal and diseased cells. While genomics offers a wide array of tools for identifying mutated or dysregulated genes, proteomics offers the ability to measure post-translational modifications, protein stability, phosphorylation state, protein-protein interactions, and protein DNA-b...

Data sharing in mass spectrometry (MS)-based proteomics is becoming a common scientific practice, as is now common in the case of other, more mature 'omics' disciplines like genomics and transcriptomics. We want to highlight that this situation, unprecedented in the field, opens a plethora of opportunities for data scientists. First, we explain in some detail some of the work already achieved, ...

Proteomics refers to a group of analytical techniques for high throughput protein analysis, providing evidence for protein expression levels, subcellular localization, post-translational modifications and molecular interactions. As such, proteomics has contributed largely to our knowledge regarding molecular mechanisms underlying health and disease and pinpointed potential disease biomarkers. T...