Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysinereactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS 3 ) have a linker arm that is 11.4 Å long when fully extended, allowing C a (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to~24 Å apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of~3 Å is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS 3 , a distance constraint of 26-30 Å between C a atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods.

Introduction The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated the problem of extracting meaningful molecular signatures of biological processes from these complex datasets. The process of biomarker discovery and characterization provides opportunities for more sophisticated approaches to integrating purely statistical and expert knowledge-based approaches. Areas covered In this review we will present examples of current practices for biomarker discovery from complex omic datasets and the challenges that have been encountered in deriving valid and useful signatures of disease. We will then present a high-level review of data-driven (statistical) and knowledge-based methods applied to biomarker discovery, highlighting some current efforts to combine the two distinct approaches. Expert opinion Effective, reproducible and objective tools for combining data-driven and knowledge-based approaches to identify predictive signatures of disease are key to future success in the biomarker field. We will describe our recommendations for possible approaches to this problem including metrics for the evaluation of biomarkers.

As data sources become larger and more complex, the ability to effectively explore and analyze patterns amongst varying sources becomes a critical bottleneck in analytic reasoning. Incoming data contains multiple variables, high signal to noise ratio, and a degree of uncertainty, all of which hinder exploration, hypothesis generation/exploration, and decision making. To facilitate the exploration of such data, advanced tool sets are needed that allow the user to interact with their data in a visual environment that provides direct analytic capability for finding data aberrations or hotspots. In this paper, we present a suite of tools designed to facilitate the exploration of spatiotemporal datasets. Our system allows users to search for hotspots in both space and time, combining linked views and interactive filtering to provide users with contextual information about their data and allow the user to develop and explore their hypotheses. Statistical data models and alert detection algorithms are provided to help draw user attention to critical areas. Demographic filtering can then be further applied as hypotheses generated become fine tuned. This paper demonstrates the use of such tools on multiple geo-spatiotemporal datasets.

D&R is a new statistical approach to the analysis of large complex data. The data are divided into subsets. Computationally, each subset is a small dataset. Analytic methods are applied to each of the subsets, and the outputs of each method are recombined to form a result for the entire data. Computations can be run in parallel with no communication among them, making them embarrassingly parallel, the simplest possible parallel processing. Using D&R, a data analyst can apply almost any statistical or visualization method to large complex data. Direct application of most analytic methods to the entire data is either infeasible, or impractical. D&R enables deep analysis: comprehensive analysis, including visualization of the detailed data, that minimizes the risk of losing important information. One of our D&R research thrusts uses statistics to develop “best” division and recombination procedures for analytic methods. Another is a D&R computational environment that has two widely used components, R and Hadoop, and our RHIPE merger of them. Hadoop is a distributed database and parallel compute engine that executes the embarrassingly parallel D&R computations across a cluster. RHIPE allows analysis wholly from within R, making programming with the data very efficient. Copyright © 2012 John Wiley & Sons, Ltd.