Plant iTRAQ-based proteomics
Abstract
We present a simple one-pot extraction protocol, which rapidly isolates hydrophyllic metabolites, lipids, and proteins from the same pulverized plant sample. Also detailed is a global plant proteomics sample preparation method utilizing iTRAQ multiplexing reagents that enables deep proteome coverage due to the use of HPLC fractionation of the peptides prior to mass spectrometric analysis. We have successfully used this protocol on several different plant tissues (e.g., roots, stems, leaves) from different plants (e.g., sorghum, poplar, Arabidopsis, soybean), and have been able to successfully detect and quantify thousands of proteins. Multiplexing strategies such as iTRAQ and the bioinformatics strategy outlined here, ultimately provide insight into which proteins are significantly changed in abundance between two or more groups (e.g., control, perturbation). Our bioinformatics strategy yields z-score values, which normalize the expression data into a format that can easily be cross-compared with other expression data (i.e., metabolomics, transcriptomics) obtained from different analytical methods and instrumentation.
- Authors:
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1406693
- Report Number(s):
- PNNL-SA-123355
Journal ID: ISBN 9781119077367; 49706; 49250; KP1601020
- DOE Contract Number:
- AC05-76RL01830
- Resource Type:
- Journal Article
- Journal Name:
- Current Protocols in Plant Biology
- Additional Journal Information:
- Journal Volume: 2; Journal Issue: 2
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; quantitative proteomics; plant; iTRAQ; Sorghum; Environmental Molecular Sciences Laboratory
Citation Formats
Handakumbura, Pubudu, Hixson, Kim K., Purvine, Samuel O., Jansson, Georg C., and Pasa Tolic, Ljiljana. Plant iTRAQ-based proteomics. United States: N. p., 2017.
Web. doi:10.1002/cppb.20052.
Handakumbura, Pubudu, Hixson, Kim K., Purvine, Samuel O., Jansson, Georg C., & Pasa Tolic, Ljiljana. Plant iTRAQ-based proteomics. United States. doi:10.1002/cppb.20052.
Handakumbura, Pubudu, Hixson, Kim K., Purvine, Samuel O., Jansson, Georg C., and Pasa Tolic, Ljiljana. Wed .
"Plant iTRAQ-based proteomics". United States. doi:10.1002/cppb.20052.
@article{osti_1406693,
title = {Plant iTRAQ-based proteomics},
author = {Handakumbura, Pubudu and Hixson, Kim K. and Purvine, Samuel O. and Jansson, Georg C. and Pasa Tolic, Ljiljana},
abstractNote = {We present a simple one-pot extraction protocol, which rapidly isolates hydrophyllic metabolites, lipids, and proteins from the same pulverized plant sample. Also detailed is a global plant proteomics sample preparation method utilizing iTRAQ multiplexing reagents that enables deep proteome coverage due to the use of HPLC fractionation of the peptides prior to mass spectrometric analysis. We have successfully used this protocol on several different plant tissues (e.g., roots, stems, leaves) from different plants (e.g., sorghum, poplar, Arabidopsis, soybean), and have been able to successfully detect and quantify thousands of proteins. Multiplexing strategies such as iTRAQ and the bioinformatics strategy outlined here, ultimately provide insight into which proteins are significantly changed in abundance between two or more groups (e.g., control, perturbation). Our bioinformatics strategy yields z-score values, which normalize the expression data into a format that can easily be cross-compared with other expression data (i.e., metabolomics, transcriptomics) obtained from different analytical methods and instrumentation.},
doi = {10.1002/cppb.20052},
journal = {Current Protocols in Plant Biology},
number = 2,
volume = 2,
place = {United States},
year = {2017},
month = {6}
}
Works referenced in this record:
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
journal, October 1999
- Gygi, Steven P.; Rist, Beate; Gerber, Scott A.
- Nature Biotechnology, Vol. 17, Issue 10
Addressing Accuracy and Precision Issues in iTRAQ Quantitation
journal, April 2010
- Karp, Natasha A.; Huber, Wolfgang; Sadowski, Pawel G.
- Molecular & Cellular Proteomics, Vol. 9, Issue 9
Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS
journal, April 2003
- Thompson, Andrew; Schäfer, Jürgen; Kuhn, Karsten
- Analytical Chemistry, Vol. 75, Issue 8
Robust and Sensitive iTRAQ Quantification on an LTQ Orbitrap Mass Spectrometer
journal, May 2008
- Bantscheff, Marcus; Boesche, Markus; Eberhard, Dirk
- Molecular & Cellular Proteomics, Vol. 7, Issue 9
Multi-omic Data Integration Links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response
journal, May 2013
- Nakayasu, Ernesto S.; Brown, Roslyn N.; Ansong, Charles
- Molecular & Cellular Proteomics, Vol. 12, Issue 8
iTRAQ-based quantitative proteomics analysis of rice leaves infected by Rice stripe virus reveals several proteins involved in symptom formation
journal, June 2015
- Wang, Biao; Hajano, Jamal-U-Ddin; Ren, Yingdang
- Virology Journal, Vol. 12, Issue 1
Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research
journal, February 2007
- Wiese, Sebastian; Reidegeld, Kai A.; Meyer, Helmut E.
- PROTEOMICS, Vol. 7, Issue 3
iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress
journal, November 2016
- Li, Qingye; Chang, Rong; Sun, Yijun
- PLOS ONE, Vol. 11, Issue 11
Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum
journal, July 2012
- Nguyen, Tran Hong Nha; Brechenmacher, Laurent; Aldrich, Joshua T.
- Molecular & Cellular Proteomics, Vol. 11, Issue 11
High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis
journal, April 2012
- Yang, Feng; Shen, Yufeng; Camp, David G.
- Expert Review of Proteomics, Vol. 9, Issue 2
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts
journal, December 2015
- Tabb, David L.; Wang, Xia; Carr, Steven A.
- Journal of Proteome Research, Vol. 15, Issue 3