Gordon A. Anderson

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UNLABELLED Data Analysis Tool Extension (DAnTE) is a statistical tool designed to address challenges associated with quantitative bottom-up, shotgun proteomics data. This tool has also been demonstrated for microarray data and can easily be extended to other high-throughput data types. DAnTE features selected normalization methods, missing value imputation(More)
MOTIVATION The size and complex nature of mass spectrometry-based proteomics datasets motivate development of specialized software for statistical data analysis and exploration. We present DanteR, a graphical R package that features extensive statistical and diagnostic functions for quantitative proteomics data analysis, including normalization, imputation,(More)
full-scale simulations will require not only petaflop capabilities but also a computational infrastructure that permits model integration. Simultaneously, it must couple to huge databases created by an ever-increasing number of high-throughput instruments. " 2 More recently, a DOE-sponsored report on visual analysis and data exploration at extreme scale 3(More)
MOTIVATION LC-MS allows for the identification and quantification of proteins from biological samples. As with any high-throughput technology, systematic biases are often observed in LC-MS data, making normalization an important preprocessing step. Normalization models need to be flexible enough to capture biases of arbitrary complexity, while avoiding(More)
MOTIVATION Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics datasets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates(More)
MOTIVATION Ion mobility spectrometry (IMS) has gained significant traction over the past few years for rapid, high-resolution separations of analytes based upon gas-phase ion structure, with significant potential impacts in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics(More)
MOTIVATION The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. RESULTS We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion(More)
We have designed and implemented a Cray XD 1-based simulation of data capture and signal processing for an advanced Ion Mobility mass spectrometer (Hadamard transform Ion Mobility). Our simulation is a hybrid application that uses both an FPGA component and a CPU-based software component to simulate Ion Mobility mass spectrometry data processing. The FPGA(More)
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