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IsobariQ: Software for Isobaric Quantitative Proteomics using IPTL, iTRAQ, and TMT

Lookup NU author(s): Dr Achim Treumann

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Abstract

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.

Publication metadata

Author(s): Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B

Publication type: Article

Publication status: Published

Journal: Journal of Proteome Research

Year: 2011

Volume: 10

Issue: 2

Pages: 913-920

Print publication date: 10/11/2010

ISSN (print): 1535-3893

ISSN (electronic): 1535-3907

Publisher: American Chemical Society

URL: http://dx.doi.org/10.1021/pr1009977

DOI: 10.1021/pr1009977

PubMed id: 21067241

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