Skip to main content

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

Publication ,  Journal Article
House, LL; Clyde, MA; Wolpert, RL
Published in: The Annals of Applied Statistics
2011

We present a novel nonparametric Bayesian approach based on Lévy 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.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

The Annals of Applied Statistics

DOI

ISSN

1932-6157

Publication Date

2011

Volume

5

Issue

2B

Start / End Page

1488 / 1511

Related Subject Headings

  • Statistics & Probability
  • 4905 Statistics
  • 1403 Econometrics
  • 0104 Statistics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
House, L. L., Clyde, M. A., & Wolpert, R. L. (2011). Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy. The Annals of Applied Statistics, 5(2B), 1488–1511. https://doi.org/10.1214/10-AOAS450
House, L. L., M. A. Clyde, and R. L. Wolpert. “Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy.” The Annals of Applied Statistics 5, no. 2B (2011): 1488–1511. https://doi.org/10.1214/10-AOAS450.
House LL, Clyde MA, Wolpert RL. Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy. The Annals of Applied Statistics. 2011;5(2B):1488–511.
House, L. L., et al. “Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy.” The Annals of Applied Statistics, vol. 5, no. 2B, 2011, pp. 1488–511. Manual, doi:10.1214/10-AOAS450.
House LL, Clyde MA, Wolpert RL. Bayesian nonparametric models for peak identification in MALDI-TOF mass spectroscopy. The Annals of Applied Statistics. 2011;5(2B):1488–1511.

Published In

The Annals of Applied Statistics

DOI

ISSN

1932-6157

Publication Date

2011

Volume

5

Issue

2B

Start / End Page

1488 / 1511

Related Subject Headings

  • Statistics & Probability
  • 4905 Statistics
  • 1403 Econometrics
  • 0104 Statistics