Protein identification and quantification from riverbank grape, Vitis riparia

comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis

Iniga S. George, Anne Y. Fennell, Paul A. Haynes*

*Corresponding author for this work

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399).

Original languageEnglish
Pages (from-to)3061-3065
Number of pages5
JournalProteomics
Volume15
Issue number17
DOIs
Publication statusPublished - 1 Sep 2015

Keywords

  • Filter Aided Sample Preparation (FASP)
  • Gas Phase Fractionation (GPF)
  • Grapevine
  • Label-free quantitative shotgun proteomics
  • Plant proteomics
  • Vitis riparia

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