Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy

DOI10.1214/10-AOAS450zbMATH Open1223.62012arXiv1107.5407MaRDI QIDQ641098FDOQ641098

Authors: Leanna L. House, Merlise A. Clyde, Robert L. Wolpert 

Publication date: 21 October 2011

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: We present a novel nonparametric Bayesian approach based on L'{e}vy Adaptive Regression Kernels (LARK) to model spectral data arising from MALDI-TOF (Matrix Assisted Laser Desorption Ionization Time-of-Flight) mass spectrometry. This model-based approach provides identification and quantification of proteins through model parameters that are directly interpretable as the number of proteins, mass and abundance of proteins and peak resolution, while having the ability to adapt to unknown smoothness as in wavelet based methods. Informative prior distributions on resolution are key to distinguishing true peaks from background noise and resolving broad peaks into individual peaks for multiple protein species. Posterior distributions are obtained using a reversible jump Markov chain Monte Carlo algorithm and provide inference about the number of peaks (proteins), their masses and abundance. We show through simulation studies that the procedure has desirable true-positive and false-discovery rates. Finally, we illustrate the method on five example spectra: a blank spectrum, a spectrum with only the matrix of a low-molecular-weight substance used to embed target proteins, a spectrum with known proteins, and a single spectrum and average of ten spectra from an individual lung cancer patient.

Full work available at URL: https://arxiv.org/abs/1107.5407

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zbMATH Keywords

waveletskernel regressionreversible jump Markov chain Monte Carlogamma random fieldLévy random fields

Mathematics Subject Classification ID

Bayesian inference (62F15) Nonparametric regression and quantile regression (62G08) Random fields; image analysis (62M40) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Biochemistry, molecular biology (92C40)

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Cited In (7)

• Bayesian model calibration for vacuum-ultraviolet photoionisation mass spectrometry
• Bayesian Analysis of Mass Spectrometry Proteomic Data Using Wavelet-Based Functional Mixed Models
• Analyze of maldi-tof proteomic spectra with usage of mixture of Gaussian distributions
• An EM-type approach for classification of bivariate MALDI-MS data and identification of high fertility markers
• Function-on-scalar quantile regression with application to mass spectrometry proteomics data
• Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy
• A Bayesian model of NMR spectra for the deconvolution and quantification of metabolites in complex biological mixtures

Uses Software

• R
• KernSmooth
• Cromwell
• PROcess
• EBayesThresh

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