Related papers: Stronger findings from mass spectral data through …
Liquid Chromatography coupled to Mass Spectrometry (LC-MS) based methods are commonly used for high-throughput, quantitative measurements of the proteome (i.e. the set of all proteins in a sample at a given time). Targeted LC-MS produces…
Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain profiles of metabolites dissolved in biofluids such as cell supernatants. Methods for estimating metabolite concentrations from these spectra are presently…
We develop a novel peak detection algorithm for the analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC$\times$GC-TOF MS) data using normal-exponential-Bernoulli (NEB) and mixture probability…
The estimation of the signal location and intensity of a peak in a pulse height spectrum is important for x-ray and $\gamma$-ray spectroscopy, charged-particle spectrometry, liquid chromatography, and many other subfields. However, both the…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
Raman spectroscopy can be used to identify molecules such as DNA by the characteristic scattering of light from a laser. It is sensitive at very low concentrations and can accurately quantify the amount of a given molecule in a sample. The…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
In this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels'…
Multilevel compositional data are data that are repeatedly measured or clustered within groups and are non-negative and sum to a constant value. These data arise in various settings, such as intensive, longitudinal studies using ecological…
In comparative proteomics studies, LC-MS/MS data is generally quantified using one or both of two measures: the spectral count, derived from the identification of MS/MS spectra, or some measure of ion abundance derived from the LC-MS data.…
MALDI mass spectrometry imaging (MALDI MSI) is a spatially resolved analytical tool for biological tissue analysis by measuring mass-to-charge ratios of ionized molecules. With increasing spatial and mass resolution of MALDI MSI data,…
The heuristic identification of peaks from noisy complex spectra often leads to misunderstanding of the physical and chemical properties of matter. In this paper, we propose a framework based on Bayesian inference, which enables us to…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
In this work, we propose a two-stage algorithm based on Bayesian modeling and computation aiming at quantifying analyte concentrations or quantities in complex mixtures with Raman spectroscopy. A hierarchical Bayesian model is built for…
The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…
Mass spectrometry (MS) is an important technique for chemical profiling which calculates for a sample a high dimensional histogram-like spectrum. A crucial step of MS data processing is the peak picking which selects peaks containing…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
Coupling a multi-capillary column (MCC) with an ion mobility (IM) spectrometer (IMS) opened a multitude of new application areas for gas analysis, especially in a medical context, as volatile organic compounds (VOCs) in exhaled breath can…
The integration of data from multiple sources is increasingly used to achieve larger sample sizes and enhance population diversity. Our previous work established that, under random sampling from the same underlying population, integrating…
Spectral clustering is a popular method for effectively clustering nonlinearly separable data. However, computational limitations, memory requirements, and the inability to perform incremental learning challenge its widespread application.…