Title : Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on
Library-Assisted eXtracted Ion Chromatogram
Author : Liang Xue et al
Date : August 1, 2013
Post : Molecular & Cellular Proteomics, 12, 2354-2369.
Link :
Abstract
Global phosphorylation changes in plants in response to environmental stress have been relatively poorly characterized to date. Here we introduce a novel mass spectrometry-based label-free quantitation method that facilitates systematic profiling plant phosphoproteome changes with high efficiency and accuracy. This method employs synthetic peptide libraries tailored specifically as internal standards for complex phosphopeptide samples and accordingly, a local normalization algorithm, LAXIC, which calculates phosphopeptide abundance normalized locally with co-eluting library peptides. Normalization was achieved in a small time frame centered to each phosphopeptide to compensate for the diverse ion suppression effect across retention time. The label-free LAXIC method was further treated with a linear regression function to accurately measure phosphoproteome responses to osmotic stress in Arabidopsis. Among 2027 unique phosphopeptides identified and 1850 quantified phosphopeptides inArabidopsis samples, 468 regulated phosphopeptides representing 497 phosphosites have shown significant changes. Several known and novel components in the abiotic stress pathway were identified, illustrating the capability of this method to identify critical signaling events among dynamic and complex phosphorylation. Further assessment of those regulated proteins may help shed light on phosphorylation response to osmotic stress in plants.
Footnotes
↵‡‡ The corresponding author is the founder and Chief Scientific Officer of Tymora Analytical.
↵* This project has been funded in part by an NSF CAREER award CHE-0645020 (W.A.T.), and by National Institutes of Health grants GM088317 (W.A.T.), GM059138 (J.-K.Z.), GM103725 (P.R.), and RR024236 (P.R.).
↵
This article contains supplemental Figs. S1 to S7 and Tables S1 to S9.
- Received January 5, 2013.
- Revision received April 18, 2013.
- © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.
Title : Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on
Library-Assisted eXtracted Ion Chromatogram
Author : Liang Xue et al
Date : August 1, 2013
Post : Molecular & Cellular Proteomics, 12, 2354-2369.
Link :
Abstract
Global phosphorylation changes in plants in response to environmental stress have been relatively poorly characterized to date. Here we introduce a novel mass spectrometry-based label-free quantitation method that facilitates systematic profiling plant phosphoproteome changes with high efficiency and accuracy. This method employs synthetic peptide libraries tailored specifically as internal standards for complex phosphopeptide samples and accordingly, a local normalization algorithm, LAXIC, which calculates phosphopeptide abundance normalized locally with co-eluting library peptides. Normalization was achieved in a small time frame centered to each phosphopeptide to compensate for the diverse ion suppression effect across retention time. The label-free LAXIC method was further treated with a linear regression function to accurately measure phosphoproteome responses to osmotic stress in Arabidopsis. Among 2027 unique phosphopeptides identified and 1850 quantified phosphopeptides inArabidopsis samples, 468 regulated phosphopeptides representing 497 phosphosites have shown significant changes. Several known and novel components in the abiotic stress pathway were identified, illustrating the capability of this method to identify critical signaling events among dynamic and complex phosphorylation. Further assessment of those regulated proteins may help shed light on phosphorylation response to osmotic stress in plants.
Footnotes
↵‡‡ The corresponding author is the founder and Chief Scientific Officer of Tymora Analytical.
↵* This project has been funded in part by an NSF CAREER award CHE-0645020 (W.A.T.), and by National Institutes of Health grants GM088317 (W.A.T.), GM059138 (J.-K.Z.), GM103725 (P.R.), and RR024236 (P.R.).
↵
This article contains supplemental Figs. S1 to S7 and Tables S1 to S9.