Analysis of rice proteins using SDS-PAGE shotgun proteomics

Karlie A. Neilson, Iniga S. George, Samantha J. Emery, Sridevi Muralidharan, Mehdi Mirzaei, Paul A. Haynes

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

13 Citations (Scopus)


In this chapter we describe the workflow used in our laboratory to analyze rice leaf samples using label-free shotgun proteomics based on SDS-PAGE fractionation of proteins. Rice proteomics has benefitted substantially from successful execution of shotgun proteomics techniques. We describe steps on how to proceed starting from rice protein extraction, SDS-PAGE, in-gel protein digestion with trypsin, nanoLC-MS/MS, and database searching using the GPM. Data from these experiments can be used for spectral counting, where simultaneous quantitation of several thousand proteins can be obtained.

Original languageEnglish
Title of host publicationPlant proteomics
Subtitle of host publicationMethods and protocols
EditorsJesus V. Jorrin-Novo, Setsuko Komatsu, Wolfram Weckwerth, Stefanie Wienkoop
Place of PublicationNew York
PublisherHumana Press Inc.
Number of pages14
ISBN (Electronic)9781627036313
ISBN (Print)9781627036306
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Label-free
  • Plant proteomics
  • Rice
  • Shotgun proteomics


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