A signature-based method to distinguish time-of-flight secondary-ion mass spectra from biological samples.

Time-Of-Flight Mass Spectrometry (TOF-SIMS) was used to determine elemental and biomolecular ions from isolated protein samples. We identified a set of 23 mass-to-charge ratio (m/z) peaks that represent signatures for distinguishing biological samples. The 23 peaks were identified by Singular Value Decomposition (SVD) and Canonical Analysis (CA) to find the underlying structure in the complex mass-spectra data sets. From this modified data, SVD was used to identify sets of m/z peaks, and we used these patterns from the TOF-SIMS data to predict the biological source from which individual mass spectra were generated. The signatures were validated using an additional data set different from the initial training set used to identify the signatures. We present a simple method to identify multiple variables required for sample classification based on mass spectra that avoids overfit. This is important in a variety of studies using mass spectrometry, including the ability to identify proteins in complex mixtures and for the identification of new biomarkers.

The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature.

Many contaminant releases to the terrestrial environment are of small areal extent. Thus, rather than evaluating the ecological impact on species in the immediate vicinity of the release, it may be more ecologically meaningful to determine if population impacts occur at the landscape level. In order to do this, the cumulative impact of all releases in the landscape under consideration must be evaluated. If the release sites are viewed as localized areas that are no longer available for use by ecological receptors (i.e., no longer part of the habitat), this can be thought of as a form of habitat fragmentation. Habitat fragmentation is typically viewed as the loss of large areas of habitat within a landscape, leaving small isolated patches of intact habitat within a hostile matrix. Small-scale contaminant releases, on the other hand, result in small uninhabitable areas within a primarily intact habitat. With this consideration in mind, we analyzed the wildlife and conservation biology literature to determine if information on habitat size requirements such as home-range or critical patch size could inform us about the potential for impact at the landscape level from release sites based on the size of the release alone. We determined that evaluating the impact of release size had to be conducted within a contextual basis (considering the existing state of the landscape). Therefore, we also reviewed the population modeling literature to determine if models could be developed to further evaluate the impact of the spatial extent of chemical releases on the landscape. We identified individual-based models linked to geographic information systems to have the greatest potential in investigating the role of release size with respect to population impacts at the landscape level.