Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete sub-complexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery.

Abstract. We prove that faithful traces on separable and nuclear C * -algebras in the UCT class are quasidiagonal. This has a number of consequences. Firstly, by results of many hands, the classification of unital, separable, simple and nuclear C * -algebras of finite nuclear dimension which satisfy the UCT is now complete. Secondly, our result links the finite to the general version of the Toms-Winter conjecture in the expected way and hence clarifies the relation between decomposition rank and nuclear dimension. Finally, we confirm the Rosenberg conjecture: discrete, amenable groups have quasidiagonal C * -algebras.

We introduce the concept of finitely coloured equivalence for unital * -homomorphisms between C * -algebras, for which unitary equivalence is the 1-coloured case. We use this notion to classify *homomorphisms from separable, unital, nuclear C * -algebras into ultrapowers of simple, unital, nuclear, Z-stable C * -algebras with compact extremal trace space up to 2-coloured equivalence by their behaviour on traces; this is based on a 1-coloured classification theorem for certain order zero maps, also in terms of tracial data.As an application we calculate the nuclear dimension of non-AF, simple, separable, unital, nuclear, Z-stable C * -algebras with compact extremal trace space: it is 1. In the case that the extremal trace space also has finite topological covering dimension, this confirms the remaining open implication of the Toms-Winter conjecture. Inspired by homotopy-rigidity theorems in geometry and topology, we derive a "homotopy equivalence implies isomorphism" result for large classes of C * -algebras with finite nuclear dimension.

We compute the nuclear dimension of separable, simple, unital, nuclear, $${\mathcal {Z}}$$ Z -stable $$\mathrm {C}^*$$ C ∗ -algebras. This makes classification accessible from $${\mathcal {Z}}$$ Z -stability and in particular brings large classes of $$\mathrm {C}^*$$ C ∗ -algebras associated to free and minimal actions of amenable groups on finite dimensional spaces within the scope of the Elliott classification programme.