Comprehensive characterization of a proteome defines a fundamental goal in proteomics. In order to maximize proteome coverage for a complex protein mixture, i.e. to identify as many proteins as possible, various different fractionation experiments are typically performed and the individual fractions are subjected to mass spectrometric analysis. The resulting data are integrated into large and h...

Proteome profiling is a type of quantitative analysis that reveals level of protein expression in the sample. Proteome profiling by using selected reaction monitoring is an approach for the Chromosome-centric Human Proteome Project (C-HPP). Here we describe dataset generated in the course of the pilot phase of Russian part of C-HPP, which was focused on human Chr 18 proteins. Proteome profiling...

Urine is a good source of biomarkers for clinical proteomics studies. However, one challenge in the use of urine biomarkers is that outside factors can affect the urine proteome. Prednisone is a commonly prescribed glucocorticoid used to treat various diseases in the clinic. To evaluate the possible impact of glucocorticoid drugs on the urine proteome, specifically disease biomarkers, this stud...

The soybean seed's protein content and composition are regulated by both genetics and physiology. Overt seed protein content is specified by the genotype's genetic framework and is selectable as a breeding trait. Within the genotype-specified protein content phenotype soybeans have the capacity to rebalance protein composition to create differing proteomes. Soybeans possess a relatively standar...

Genome-scale metabolic models (GEMs) are widely used to predict phenotypes with the aid of constraint-based modeling. In order improve predictive power these models, there have been many efforts on imposing biological constraints, among which proteome constraints particular interest. Here we describe concept and review proteome-constrained GEMs, as well their advantages applications. addition, ...

Despite the complete determination of the genome sequence of several higher eukaryotes, their proteomes remain relatively poorly defined. Information about proteins identified by different experimental and computational methods is stored in different databases, meaning that no single resource offers full coverage of known and predicted proteins. IPI (the International Protein Index) has been de...

The Bacteroides fragilis NCTC 9343 genome is the fifth member of the Bacteroidetes/ Chlorobi group to be sequenced and the second Bacteroides fragilis strain. The Bacteroides fragilis NCTC 9343 genome shows considerable variation even within the same strain and ‘invertable promoters’ appear to regulate much of this variance in many surface-exposed and secreted proteins (Cerdeño-Tárraga et al., ...

Definition 1. A hybrid planning problem (HPP) 〈s0,Γ,A〉 is specified by an initial state s0 ∈ S, a finite goal set of constraints Γ, and a set of actions A. Definition 2. A finite sequence of actions (a1, a2, ..., am) ∈ A×A× ... is a solution to an HPP if and only if the corresponding sequence of states (s0, s1, ..., sm) ∈ S starting from s0 and recursively constructed using si = ai.eff (si−1) s...

specific variations in sarcoplasmic proteome influence beef color. Post-mortem aging is a common practice employed by beef industry for improving beef tenderness and palatability. However, the color attributes and sarcoplasmic proteome of beef muscles undergo changes during aging. The objective of this study was to examine the changes in the sarcoplasmic proteome profile of three differentially...

Protein turnover is a neglected dimension in postgenomic studies, defining the dynamics of changes in protein expression and forging a link between transcriptome, proteome and metabolome. Recent advances in postgenomic technologies have led to the development of new proteomic techniques to measure protein turnover on a proteome-wide scale. These methods are driven by stable isotope metabolic la...