UNLABELLED: Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data. AVAILABILITY: online data processing service is available at http://www.nbpp.nl/warp2d.html. Taverna workflow is available at myExperiment with title '2D Time Alignment-Webservice and Workflow' at http://www.myexperiment.org/workflows/1283.html. Command line tool is available at http://www.nbpp.nl/Warp2D_commandline.zip. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Mass spectrometry data are subjected to considerable noise. Good noise models are required for proper detection and quantification of peptides. We have characterized noise in both quadrupole time-of-flight (Q-TOF) and ion trap data, and have constructed models for the noise. RESULTS: We find that the noise in Q-TOF data from Applied Biosystems QSTAR fits well to a combination of multinomial and Poisson model with detector dead-time correction. In comparison, ion trap noise from Agilent MSD-Trap-SL is larger than the Q-TOF noise and is proportional to Poisson noise. We then demonstrate that the noise model can be used to improve deisotoping for peptide detection, by estimating appropriate cutoffs of the goodness of fit parameter at prescribed error rates. The noise models also have implications in noise reduction, retention time alignment and significance testing for biomarker discovery.

We describe a visualization system designed for interactive study of proteins in the field of computational biology. Our system incorporates multiple, custom, three-dimensional and two-dimensional linked views of the proteins. We take advantage of modem commodity graphics cards, which are typically designed for games rather than scientific visualization applications, to provide instantaneous linking between views and three-dimensional interactivity on standard personal computers. Furthermore, we anticipate the usefulness of game techniques such as bump maps and skinning for scientific applications.

Geometric models are often annotated to provide additional information during visualization. Maps may be marked with rivers, roads or topographical information, and CAD data models may highlight the underlying mesh structure. While this additional information may be extremely useful, there is a rendering cost associated with it. Texture maps have often been used to convey this information at relatively low cost, but they suffer from blurring and pixelization at high magnification. We present a technique for simplifying surface annotations based on directed, asymmetric tolerance. By maintaining the annotations as geometry, as opposed to textures, we are able to simplify them while still maintaining the overall appearance of the model over a wide range of magnifications. Texture maps may still be used to provide low-resolution surface detail, such as color. We demonstrate a significant gain in rendering performance while retaining the original appearance of objects from many application domains.