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Significance Testing of Normalized LC-MS Data

By Ann Christine Catlin

Purdue University

Several statistical significance tests are employed to identify peptide or metabolite peaks that either make significant contributions to the molecular profile of a sample or distinguish a group of samples from others.

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Version 2.2 - published on 19 Sep 2011

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Abstract

The Significance Test Tool uses several statistical significance test methods to identify data elements that either contribute to the proteomic profile of a sample or that distinguish groups of samples. Some peaks may be present across sample groups but with differing intensity between the groups. The quantitative difference identifies the case where a peak is present in most (or all) samples, but with different intensities from group to group.

Methods implemented in the tool include:

  • Two-tailed t-test and
  • Mann-Whitney tests.



Input for the Significance Test Tool includes:

  • the normalized data file generated from the Normalization Tool for a collection of LC-MS datasets aligned through the Peak Alignmend Tool.
  • input parameters to provide information about the number of groups and group sizes in the normalized dataset.



credits

The significance software was developed by Xiang Zhang, Jiri Adamec, et al. in 2005.

The Purdue Discovery Pipeline was created by the Bindley Biosciences Center under the direction of Charles Buck.

The integration of Purdue Discovery Pipeline models as cceHUB tools and the contribution of test datasets to the cceHUB respository are part of a collaborative effort with Jiri Adamec, Amber Jannasch and Catherine P. Riley of the Bindley Biosciences Center and George Howlett of the Rosen Center for Advanced Computing.
Cite this work

Researchers should cite this work as follows:

  • Ann Christine Catlin (2011), "Significance Testing of Normalized LC-MS Data," http://ccehub.org/resources/significance.

    BibTex | EndNote

Tags
  1. proteome discovery pipeline
  2. proteomics
  3. statistical significance