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J Biomol Tech. 2010 September; 21(3 Suppl): S10.
PMCID: PMC2918090

Leveraging Technologies: DIGE and MudPIT

H. McDonald
Vanderbilt University, Nashville, TN, United States

Abstract

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Several different technology platforms exist that can provide information on over 1,000 proteins in a given assay. They each bring some important strengths and unfortunate weaknesses to a proteomics experiment; these differences become even more evident in the realm of quantitative proteomics where technical noise can play a large role in obscuring biological-significance. We are using an adaptive sample size re-estimation approach to leverage the statistical power associated with a DIGE-MS experiment (where independent biological replicates from multiple conditions can be co-analyzed with low technical noise and high statistical power) into a more sensitive MudPIT (multidimensional LC-MS/MS) experiment where additional quantitative information is accessible. These MudPIT analyses would otherwise not be able to approach the quantitative and statistical rigor of the DIGE platform without prohibitively large numbers of replicate analyses. A discussion of biological signal vs. technical/biological noise associated with proteomics experiments will be presented, along with some practical examples where these two complementary technologies have been combined to address the same biological question.


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