High-throughput peptide quantification using mTRAQ reagent triplex
- High-throughput peptide quantification using mTRAQ reagent triplex
- 윤주영; 염정훈; 이희범; 김규태; 나승진; 박근수; 백은옥; 이철주
- Issue Date
- BMC bioinformatics. [electronic resource]
- VOL 12, NO s1, s46-1-s46-12
- 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.
- Appears in Collections:
- KIST Publication > Article
- Files in This Item:
There are no files associated with this item.
- RIS (EndNote)
- XLS (Excel)
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.