Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

Macromolecular assemblies involving membrane proteins (MPs) serve vital biological roles and are prime drug targets in a variety of diseases. Large-scale affinity purification studies of soluble-protein complexes have been accomplished for diverse model organisms, but no global characterization of MP-complex membership has been described so far. Here we report a complete survey of 1,590 putative integral, peripheral and lipid-anchored MPs from Saccharomyces cerevisiae, which were affinity purified in the presence of non-denaturing detergents. The identities of the co-purifying proteins were determined by tandem mass spectrometry and subsequently used to derive a high-confidence physical interaction map encompassing 1,726 membrane protein-protein interactions and 501 putative heteromeric complexes associated with the various cellular membrane systems. Our analysis reveals unexpected physical associations underlying the membrane biology of eukaryotes and delineates the global topological landscape of the membrane interactome.

Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization.

Bioactive molecules typically mediate their biological effects through direct physical association with one or more cellular proteins. The detection of drug-target interactions is therefore essential for the characterization of compound mechanism of action and off-target effects, but generic label-free approaches for detecting binding events in biological mixtures have remained elusive. Here, we report a method termed target identification by chromatographic co-elution (TICC) for routinely monitoring the interaction of drugs with cellular proteins under nearly physiological conditions in vitro based on simple liquid chromatographic separations of cell-free lysates. Correlative proteomic analysis of drug-bound protein fractions by shotgun sequencing is then performed to identify candidate target(s). The method is highly reproducible, does not require immobilization or derivatization of drug or protein, and is applicable to diverse natural products and synthetic compounds. The capability of TICC to detect known drug-protein target physical interactions (K(d) range: micromolar to nanomolar) is demonstrated both qualitatively and quantitatively. We subsequently used TICC to uncover the sterol biosynthetic enzyme Erg6p as a novel putative anti-fungal target. Furthermore, TICC identified Asc1 and Dak1, a core 40 S ribosomal protein that represses gene expression, and dihydroxyacetone kinase involved in stress adaptation, respectively, as novel yeast targets of a dopamine receptor agonist.

Assessing the matrix effects of hemolyzed samples in bioanalysis.

Validation of LC-MS/MS assays includes an assessment of matrix effects. Hemolysis effect, a special type of matrix effect, can also have an impact on analyte quantitation. In situations where the hemolysis effect is marginal, this can be resolved simply by dilution of hemolyzed samples with plasma prior to analysis. However, in some cases, the impact can be so dramatic that analytes are completely immeasurable. In such situations, modification to the bioanalytical method will be required, including, but not limited to, adjusting the chromatographic conditions to separate interferences present in hemolyzed samples; additional sample clean-up techniques such as protein precipitation in combination with SPE or a change in extraction technique such as from SPE to a liquid-liquid extraction method. Here, we report examples from four bioanalytical methods, where the presence of hemolyzed blood in plasma was found to have an impact on analyte quantitation and a description of the solutions adopted to resolve this are provided.

Determination of carryover and contamination for mass spectrometry-based chromatographic assays.

The Third American Association of Pharmaceutical Scientists/Food and Drug Administration Bioanalytical Workshop, held in 2006, reviewed and evaluated current practices and proposed that carryover and contamination be assessed not only during the validation of an assay but also during the application of the method in a study. In this article, the potential risks of carryover and contamination in each stage of a bioanalytical method are discussed, to explain to the industry why this recommendation is being made.