Absolute protein quantification by LC/MS(E) for global analysis of salicylic acid-induced plant protein secretion responses

J Proteome Res. 2009 Jan;8(1):82-93. doi: 10.1021/pr800649s.


The plant cell wall is a dynamic cellular compartment consisting of a complex matrix of components that can change dramatically in response to environmental stresses. During pathogen attack, for instance, a wide spectrum of proteins that participate in various sequential processes involved in plant defense is secreted into the cell wall. In this study, a mass spectrometry, data-independent acquisition approach known as LC/MS (E) was used to assess temporal changes in the cell wall proteome in response to different levels of an endogenous inducer of plant disease defense responses, salicylic acid (SA). LC/MS (E) was used as a label-free method that enabled simultaneous protein identification and absolute femtomole quantification of each protein secreted into the extracellular matrix. A total of 74 secreted proteins were identified, 63 of which showed increased specific secretion in response to SA. A majority of this induced secretion occurred within 2 h of treatment, indicating that many proteins are involved in the early stages of plant defenses. We also identified a number of apparently nonclassically secreted proteins, suggesting that, as in many nonplant systems, Golgi/ER-independent mechanisms exist for plant protein secretion. These results provide new insight into plant apoplastic defense mechanisms and demonstrate that LC/MS (E) is a powerful tool for obtaining both relative and absolute proteome-scale quantification that can be applied to complex, time- and dose-dependent experimental designs.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / drug effects*
  • Arabidopsis / metabolism
  • Chromatography, Liquid / methods*
  • Computational Biology
  • Mass Spectrometry / methods*
  • Plant Physiological Phenomena
  • Plant Proteins / metabolism*
  • Proteins / metabolism
  • Proteome
  • Proteomics / methods*
  • Salicylic Acid / metabolism
  • Salicylic Acid / pharmacology*
  • Time Factors


  • Plant Proteins
  • Proteins
  • Proteome
  • Salicylic Acid