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BackgroundTranslational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the most tightly controlled entities by selective degradation of their individual proteins. They furthermore act as control hubs that regulate highly important processes in the cell and exhibit a high functional diversity due to their ability to change their composition and their structure. Better understanding and prediction of these functional states demands methods for the characterization of complex composition, behavior, and abundance across multiple cell states. Mass spectrometry provides an unbiased approach to directly determine protein abundances across different cell populations and thus to profile a comprehensive abundance map of proteins.ResultsWe provide a tool to investigate the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. Thorough assessment of different randomization methods and statistical scoring algorithms allows determining the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types as well as the identification of intrinsic structures in complex behavior to determine which proteins orchestrate complex function. This analysis can be extended to investigate common profiles within arbitrary protein groups. CoExpresso can be accessed through http://computproteomics.bmb.sdu.dk/Apps/CoExpresso.ConclusionsWith the CoExpresso web service, we offer a potent scoring scheme to assess proteins for their co-regulation and thereby offer insight into their potential for forming functional groups like protein complexes., QC 20190129

Proteomics is a highly dynamic field driven by frequent introduction of new technological approaches, leading to high demand for new software tools and the concurrent development of many methods for data analysis, processing, and storage. The rapidly changing landscape of proteomics software makes finding a tool fit for a particular purpose a significant challenge. The comparison of software and the selection of tools capable to perform a certain operation on a given type of data rely on their detailed annotation using well-defined descriptors. However, finding accurate information including tool input/output capabilities can be challenging and often heavily depends on manual curation efforts. This is further hampered by a rather low half-life of most of the tools, thus demanding the maintenance of a resource with updated information about the tools. We present here our approach to curate a collection of 189 software tools with detailed information about their functional capabilities. We furthermore describe our efforts to reach out to the proteomics community for their engagement, which further increased the catalog to >750 tools being about 70% of the estimated number of 1097 tools existing for proteomics data analysis. Descriptions of all annotated tools are available at http://proteomics.bio.tools.

The effects of complimentary compound feeds with varying protein levels on growth performance, feed utilization, and whole body composition were studied in golden grey mullet, Liza aurata. Fish of initial weight 51.15.2 g were raised in hapas in a coastal lagoon and fed four iso-energetic diets containing 25%, 30%, 35% or 45% of crude protein for 20 weeks. L. aurata reared on the experimental diets showed relatively low growth rates (SGR ranged from 0.40 to 0.48%/day, and feed utilization parameters (FE ranged from 0.27 to 0.34) among dietary groups consistent with the known slow growth rate of the species. The growth performance and feed utilization of L. aurata was not significantly affected by dietary protein level, despite the fact that there was a trend indicating better fish growth and feed efficiency with increasing dietary protein level. This is indicative of the low protein requirements of L. aurata, although it could be that higher dietary protein concentrations could possibly improve growth performance. The farming of low-trophic species such as L. aurata allows under-utilized trophic resources to be better exploited for fish production. Thus any future advances in understanding the nutrition and feeding of L. aurata under culture conditions, could improve further the potential of this species, especially in regional and coastal aquaculture.