No abstract

Complete reference maps or datasets, like the genomic map of an organism, are highly beneficial tools for biological and biomedical research. Attempts to generate such reference datasets for a proteome so far failed to reach complete proteome coverage, with saturation apparent at approximately two thirds of the proteomes tested, even for the most thoroughly characterized proteomes. Here, we used a strategy based on high-throughput peptide synthesis and mass spectrometry to generate a close to complete reference map (97% of the genome-predicted proteins) of the S. cerevisiae proteome. We generated two versions of this mass spectrometric map one supporting discovery- (shotgun) and the other hypothesis-driven (targeted) proteomic measurements. The two versions of the map, therefore, constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. The reference libraries can be browsed via a web-based repository and associated navigation tools. To demonstrate the utility of the reference libraries we applied them to a protein quantitative trait locus (pQTL) analysis, which requires measurement of the same peptides over a large number of samples with high precision. Protein measurements over a set of 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, impacting on the levels of related proteins. Our results suggest that selective pressure favors the acquisition of sets of polymorphisms that maintain the stoichiometry of protein complexes and pathways.

A strong signal for double parton (DP) scattering is observed in a 16 pb(-1) sample of <(p)over bar p> --> gamma/pi(0) + 3 jets + X data from the CDF experiment at the Fermilab Tevatron. In DP events, two separate hard scatterings take place in a single <(p)over bar p> collision. We isolate a large sample of data (similar to 14 000 events) of which 53% are found to be DP. The process-independent parameter of double parton scattering, sigma(eff), is obtained without reference to theoretical calculations by comparing observed DP events to events with hard scatterings in separate <(p)over bar p> collisions. The result sigma(eff) = (14.5 +/- 1.7(-2.3)(+1.7)) mb represents a significant improvement over previous measurements, and is used to constrain simple models of parton spatial density. The Feynman x dependence of sigma(eff) is investigated and none is apparent. Further, no evidence is found for kinematic correlations between the two scatterings in DP events