Table 1. Cleavage rule Digesting Reagent C Armillaria B AspN B Thermolysin B Clostripain A LysC A Pancreatic Elastase A Digesting Reagent C CNBr_Cys { Chymotrypsin A if Trypsin A V8 Ammonium Acetate A V8 Phosphate Buffer A Hydroxylamine A Mild Acid Hydrolysis A We present a stochastic model of proteolytic digestion of a proteome, assuming the distribution of parent protein lengths in the proteo...

Listeria monocytogenes is a foodborne pathogen capable of surviving under challenging conditions both outside and inside the host. During the transition from exponential to stationary phase it experiences a series of environmental changes that require an appropriate response to maintain cell viability. In this study the autolytic behaviour of a L. monocytogenes strain was investigated by two-di...

Running Title Towards a confocal subcellular atlas of the human proteome Towards a confocal subcellular atlas of the human proteome

Quantitative proteomics involves the identification and quantitation of protein components in various biological systems. Stable isotope labelling technology, by both metabolic and chemical methods, has been the most commonly used approach for global proteome-wide profiling. Recently, its capability has been extended from labelled pairs to multiple labels, allowing for the simultaneous quantifi...

The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes (http://www.ebi.ac. uk/proteome/). The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (In...

The complexity of proteomes makes good experimental design essential for their successful investigation. Here, we describe how proteomics experiments can be modeled and how computer simulations of these models can be used to improve experimental designs.

A plane poset is a finite set with two partial orders, satisfying a certain incompatibility condition. The set PP of isoclasses of plane posets owns two products, and an infinitesimal Hopf algebra structure is defined on the vector space HPP generated by PP , using the notion of biideals of plane posets. We here define a partial order on PP , making it isomorphic to the set of partitions with t...

Intrinsically disordered proteins are highly abundant in various proteomes. They are different from ordered proteins at many levels, and their structural and functional characterization requires special experimental and computational tools.

The human eye proteome is the latest addition to the HUPO Human Proteome Project (HPP). Semba et al. (The Human Eye Proteome Project: Perspectives on an emerging proteome. Proteomics 2013, 13, 2500-2511) establish a provisional baseline for the proteomes of the many anatomical compartments of the eye, based on literature review. As part of the Biology and Disease-driven HPP, they and their coll...

The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characteri...