title: Analysis of rice proteins using SDS-PAGE shotgun proteomics.
abstract: 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.
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Karlie A
authors.initials: KA
authors.lastname: Neilson
authors.forename: Iniga S
authors.initials: IS
authors.lastname: George
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Emery
authors.forename: Sridevi
authors.initials: S
authors.lastname: Muralidharan
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaei
authors.forename: Paul A
authors.initials: PA
authors.lastname: Haynes
mesh_terms: D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D013058:Mass Spectrometry; D036103:Nanotechnology; D012275:Oryza / Q000378:metabolism*; D010455:Peptides / Q000032:analysis; D010940:Plant Proteins / Q000032:analysis* / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D010940:Plant Proteins