3DSpectra

A 3-dimensional quantification algorithm for LC–MS labeled profile data
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Updated 22 Sep 2014

This is the Matlab code related to the research project published in the paper "3DSpectra: A 3-dimensional quantification algorithm for LC–MS labeled profile data": http://www.sciencedirect.com/science/article/pii/S1874391914004163
Summary
Mass spectrometry-based proteomics can generate highly informative datasets, as profile three-dimensional (3D) LC–MS data: LC–MS separates peptides in two dimensions (time, m/z) minimizing their overlap, and profile acquisition enhances quantification. To exploit both data features, we developed 3DSpectra, a 3D approach embedding a statistical method for peptide border recognition.

3DSpectra efficiently accesses profile data by means of mzRTree, and makes use of a priori metadata, provided by search engines, to quantify the identified peptides. An isotopic distribution model, shaped by a bivariate Gaussian Mixture Model (GMM), which includes a noise component, is fitted to the peptide peaks using the expectation–maximization (EM) approach. The EM starting parameters, i.e., the centers and shapes of the Gaussians, are retrieved from the metadata. The borders of the peaks are delimited by the GMM iso-density curves, and noisy or outlying data are discarded from subsequent analysis.

The 3DSpectra program was compared to ASAPRatio for a controlled mixture of Isotope-Coded Protein Labels (ICPL) labeled proteins, which were mixed at predefined ratios and acquired in enhanced profile mode, in triplicate. The 3DSpectra software showed significantly higher linearity, quantification accuracy, and precision than did ASAPRatio in this real use case simulation where the true ratios are known, and it also achieved wider peptide coverage and dynamic range.

Cite As

Sara Nasso (2024). 3DSpectra (https://github.com/saranasso/3DSpectra), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2011a
Compatible with any release
Platform Compatibility
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Version Published Release Notes
1.0.0.0

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.