Bioinformatics Advance Access originally published online on August 13, 2007
Bioinformatics 2007 23(19):2528-2535; doi:10.1093/bioinformatics/btm385
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Improved model-based, platform-independent feature extraction for mass spectrometry
1Integrated Data System Department, Siemens Corporate Research, 755 College Road East, Princeton, NJ 08540, USA and 2Life Sciences Department, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Motivation: Mass spectrometry (MS) is increasingly being used for biomedical research. The typical analysis of MS data consists of several steps. Feature extraction is a crucial step since subsequent analyses are performed only on the detected features. Current methodologies applied to low-resolution MS, in which features are peaks or wavelet functions, are parameter-sensitive and inaccurate in the sense that peaks and wavelet functions do not directly correspond to the underlying molecules under observation. In high-resolution MS, the model-based approach is more appealing as it can provide a better representation of the MS signals by incorporating information about peak shapes and isotopic distributions. Current model-based techniques are computationally expensive; various algorithms have been proposed to improve the computational efficiency of this paradigm. However, these methods cannot deal well with overlapping features, especially when they are merged to create one broad peak. In addition, no method has been proven to perform well across different MS platforms.
Results: We suggest a new model-based approach to feature extraction in which spectra are decomposed into a mixture of distributions derived from peptide models. By incorporating kernel-based smoothing and perceptual similarity for matching distributions, our statistical framework improves existing methodologies in terms of computational efficiency and the accuracy of the results. Our model is parameterized by physical properties and is therefore applicable to different MS instruments and settings. We validate our approach on simulated data, and show that the performance is higher than commonly used tools on real high- and low-resolution MS, and MS/MS data sets.
Contact: daniel.fasulo{at}siemens.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Associate Editor: John Quackenbush
Received on February 26, 2007; revised on June 25, 2007; accepted on July 19, 2007
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Wang, X. Zhou, H. Wang, K. Li, L. Yao, and S. T.C. Wong Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model Bioinformatics, July 1, 2008; 24(13): i407 - i413. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Barla, G. Jurman, S. Riccadonna, S. Merler, M. Chierici, and C. Furlanello Machine learning methods for predictive proteomics Brief Bioinform, March 1, 2008; 9(2): 119 - 128. [Abstract] [Full Text] [PDF]
|
|