RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data.

Metabolomic data are frequently acquired using chromatographically coupled mass spectrometry (MS) platforms. For such datasets, the first step in data analysis relies on feature detection, where a feature is defined by a mass and retention time. While a feature typically is derived from a single compound, a spectrum of mass signals is more a more-accurate representation of the mass spectrometric signal for a given metabolite. Here, we report a novel feature grouping method that operates in an unsupervised manner to group signals from MS data into spectra without relying on predictability of the in-source phenomenon. We additionally address a fundamental bottleneck in metabolomics, annotation of MS level signals, by incorporating indiscriminant MS/MS (idMS/MS) data implicitly: feature detection is performed on both MS and idMS/MS data, and feature-feature relationships are determined simultaneously from the MS and idMS/MS data. This approach facilitates identification of metabolites using in-source MS and/or idMS/MS spectra from a single experiment, reduces quantitative analytical variation compared to single-feature measures, and decreases false positive annotations of unpredictable phenomenon as novel compounds. This tool is released as a freely available R package, called RAMClustR, and is sufficiently versatile to group features from any chromatographic-spectrometric platform or feature-finding software.

Association of human immune response to Aedes aegypti salivary proteins with dengue disease severity.

Dengue viruses (DENV; family Flaviviridae, genus Flavivirus) are transmitted by Aedes aegypti mosquitoes and can cause dengue fever (DF), a relatively benign disease, or more severe dengue haemorrhagic fever (DHF). Arthropod saliva contains proteins delivered into the bite wound that can modulate the host haemostatic and immune responses to facilitate the intake of a blood meal. The potential effects on DENV infection of previous exposure to Ae. aegypti salivary proteins have not been investigated. We collected Ae. aegypti saliva, concentrated the proteins and fractionated them by nondenaturing polyacrylamide gel electrophoresis (PAGE). By the use of immunoblots, we analysed reactivity with the mosquito salivary proteins (MSP) of sera from 96 Thai children diagnosed with secondary DENV infections leading either to DF or DHF, or with no DENV infection, and found that different proportions of each patient group had serum antibodies reactive to specific Ae. aegypti salivary proteins. Our results suggest that prior exposure to MSP might play a role in the outcome of DENV infection in humans.

Proteomic analysis of diaminochlorotriazine adducts in wistar rat pituitary glands and LbetaT2 rat pituitary cells.

Atrazine (ATRA) is the most commonly applied herbicide in the United States and is frequently detected in drinking water at significant levels. After oral exposure, ATRA metabolism yields diaminochlorotriazine (DACT), an electrophilic molecule that has been shown to form covalent protein adducts. This research was designed to identify ATRA-induced protein adducts formed in the pituitary gland of ATRA-exposed rats and in DACT-exposed LbetaT2 rat pituitary cells. Immunohistochemistry showed diffuse cytoplasmic and nuclear staining in both pituitary sections and LbetaT2 cells indicating the formation of DACT protein adducts. Protein targets from both rat pituitaries and LbetaT2 cell culture were identified following two-dimensional electrophoresis (2DE), immunodetection, and matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis. Western blots from both exposed rats and LbetaT2 cells revealed over 30 DACT-modified spots that were not present in control animals. Protein spots were matched to concurrently run 2DE gels stained with Sypro Ruby, excised, and in-gel-digested with trypsin. Mass spectrometry analysis of digest peptides resulted in the identification of 19 spots and 8 unique proteins in the rats and 21 spots and 19 unique proteins in LbetaT2 cells. The identified proteins present in both sample types included proteasome activator complex subunit 1, ubiquitin carboxyl-terminal hydrolase isozyme L1, tropomyosin, ERp57, and RNA-binding proteins. Each of these proteins contains active-site or solvent-exposed cysteine residues, making them viable targets for covalent modification by DACT.