High-throughput peptide quantification using mTRAQ reagent triplex

Title
High-throughput peptide quantification using mTRAQ reagent triplex
Authors
윤주영염정훈이희범김규태나승진박근수백은옥이철주
Issue Date
2011-02
Publisher
BMC bioinformatics. [electronic resource]
Citation
VOL 12, NO s1, s46-1-s46-12
Abstract
Background: Protein quantification is an essential step in many proteomics experiments. A number of labeling approaches have been proposed and adopted in mass spectrometry (MS) based relative quantification. The mTRAQ, one of the stable isotope labeling methods, is amine-specific and available in triplex format, so that the sample throughput could be doubled when compared with duplex reagents. Methods and results: Here we propose a novel data analysis algorithm for peptide quantification in triplex mTRAQ experiments. It improved the accuracy of quantification in two features. First, it identified and separated triplex isotopic clusters of a peptide in each full MS scan. We designed a schematic model of triplex overlapping isotopic clusters, and separated triplex isotopic clusters by solving cubic equations, which are deduced from the schematic model. Second, it automatically determined the elution areas of peptides. Some peptides have similar atomic masses and elution times, so their elution areas can have overlaps. Our algorithm successfully identified the overlaps and found accurate elution areas. We validated our algorithm using standard protein mixture experiments. Conclusions: We showed that our algorithm was able to accurately quantify peptides in triplex mTRAQ experiments. Its software implementation is compatible with Trans-Proteomic Pipeline (TPP), and thus enables highthroughput analysis of proteomics data.
URI
http://pubs.kist.re.kr/handle/201004/45649
ISSN
1471-2105
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KIST Publication > Article
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