Skip Navigation



Briefings in Functional Genomics and Proteomics Advance Access published online on April 4, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln017
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplementary Data
Right arrow All Versions of this Article:
7/2/119    most recent
eln017v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Lacerda, C. M.R.
Right arrow Articles by Reardon, K. F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lacerda, C. M.R.
Right arrow Articles by Reardon, K. F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2008. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

Analysis of iTRAQ data using Mascot and Peaks quantification algorithms

Carla M.R. Lacerda, Lei Xin, Iain Rogers and Kenneth F. Reardon

Corresponding author. Kenneth F. Reardon, Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA. Tel: 970 491 6505; Fax: 970 491 7369; Email: kenneth.reardon{at}colostate.edu

The field of proteomics has been developing rapidly toward quantification of proteins. Despite the variety of experimental techniques available for peptide and protein labelling, there are few commercially available analytical tools with the ability to interpret data from any mass spectrometer. In this study, we compare two software packages, Mascot and Peaks, for the analysis of iTRAQ data from ESI-Q/TOF mass spectrometry. In the case of a six-protein mixture combined in a known proportion, the output of the Peaks algorithm deviated from the correct result by 14% on average, while the error of the Mascot quantification was nearly 200%. When the software were used to analyse iTRAQ data from a complex protein sample, the quantification results agreed within 20% for only 26% of the quantified proteins, showing significant differences in the two quantification algorithms. This comparison and analysis revealed major intricacies in peptide and protein quantification that must be taken into consideration for software development.

Keywords: quantitative proteomics, iTRAQ, Mascot, Peaks


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.