Metabolite differentiation and discovery lab (MeDDL): a new tool for biomarker discovery and mass spectral visualization.

The goal of this work was to design and implement a prototype software tool for the visualization and analysis of small molecule metabolite GC-MS and LC-MS data for biomarker discovery. The key features of the Metabolite Differentiation and Discovery Lab (MeDDL) software platform include support for the manipulation of large data sets, tools to provide a multifaceted view of the individual experimental results, and a software architecture amenable to modification and addition of new algorithms and software components. The MeDDL tool, through its emphasis on visualization, provides unique opportunities by combining the following: easy use of both GC-MS and LC-MS data; use of both manufacturer specific data files as well as netCDF (network Common Data Form); preprocessing (peak registration and alignment in both time and mass); powerful visualization tools; and built in data analysis functionality.

Changes in volatile compounds of mouse urine as it ages: their interactions with water and urinary proteins.

Mice release a variety of chemical signals, particularly through urine, which mediate social interactions and endocrine function. Studies have been conducted to investigate the stability of urinary chemosignals in mice. Neuroendocrine and behavioral responses of mice to urine samples of male and female conspecifics which have aged for different amounts of time have been examined, demonstrating that the quality and intensity of signaling molecules in urine change over time. In this study, we monitored changes in volatile organic compounds (VOCs) released from male and female mouse urine following aging the urine samples. Substantial amounts of some VOCs were lost during the aging process of urine, whereas other VOCs increased. Considerable portions of the VOCs which exhibited the increased release were shown to have previously been dissolved in water and subsequently released as the urine dried. We also demonstrated that some VOCs decreased slightly due to their binding with the major urinary proteins (MUPs) and identified MUP ligands whose headspace concentrations increased as the urine aged. Our results underscore the important role of MUPs and the hydration status in the release of VOCs in urine, which may largely account for the changes in the quality and intensity of urinary signals over time.

Changes in volatile compounds of human urine as it ages: their interaction with water.

The urinary odors are commonly perceived as unpleasant. While numerous studies have identified the volatile organic compounds (VOCs) released from urine, the odorants responsible for the urine odor are not well characterized. Furthermore, anecdotal reports suggest that the odor of aged urine is different from that of fresh urine. However, no study has yet to investigate the specific VOCs released from aged urine. In this study, we analyzed and compared the VOCs released from fresh and aged urine samples, investigating the changes in the urinary VOCs as urine aged. We found an overall decrease in concentration of many urinary VOCs, and concluded this was due to the urine evaporating as it aged. On the contrary, some highly water-soluble compounds such as short and branched-chain organic acids and trimethylamine, increased. Their increased release is most likely due to the loss of water and the subsequent release of water-soluble VOCs as urine ages. We suggest that these VOCs may contribute to the odor of the aged urine.

Differential binding between volatile ligands and major urinary proteins due to genetic variation in mice.

Two different structural classes of chemical signals in mouse urine, i.e., volatile organic compounds (VOCs) and the major urinary proteins (MUPs), interact closely because MUPs sequester VOCs. Although qualitative and/or quantitative differences in each chemical class have been reported, previous studies have examined only one of the classes at a time. No study has analyzed these two sets simultaneously, and consequently binding interactions between volatile ligands and proteins in urines of different strains have not been compared. Here, we compared the release of VOCs in male urines of three different inbred strains (C57BL/6J, BALB/b and AKR) before and after denaturation of urinary proteins, mainly MUPs. Both MUP and VOC profiles were distinctive in the intact urine of each strain. Upon denaturation, each of the VOC profiles changed due to the release of ligands previously bound to MUPs. The results indicate that large amounts of numerous ligands are bound to MUPs and that these ligands represent a variety of different structural classes of VOCs. Furthermore, the degree of release in each ligand was different in each strain, indicating that different ligands are differentially bound to proteins in the urines of different strains. Therefore, these data suggest that binding interactions in ligands and MUPs differ between strains, adding yet another layer of complexity to chemical communication in mice.