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Statistical inference from multiple iTRAQ experiments without using common reference standards.


ABSTRACT: Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple experiments. In this manuscript, we show that using a masterpool is counterproductive. We obtain more precise estimates of protein relative abundance by using the available biological data instead of the masterpool and do not need to occupy a channel that could otherwise be used for another biological sample. In addition, we introduce a simple statistical method to associate proteomic data from multiple iTRAQ experiments with a numeric response and show that this approach is more powerful than the conventionally employed masterpool-based approach. We illustrate our methods using data from four replicate iTRAQ experiments on aliquots of the same pool of plasma samples and from a 406-sample project designed to identify plasma proteins that covary with nutrient concentrations in chronically undernourished children from South Asia.

SUBMITTER: Herbrich SM 

PROVIDER: S-EPMC4223774 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Statistical inference from multiple iTRAQ experiments without using common reference standards.

Herbrich Shelley M SM   Cole Robert N RN   West Keith P KP   Schulze Kerry K   Yager James D JD   Groopman John D JD   Christian Parul P   Wu Lee L   O'Meally Robert N RN   May Damon H DH   McIntosh Martin W MW   Ruczinski Ingo I  

Journal of proteome research 20130116 2


Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple ex  ...[more]

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