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 journalArticlepeer-review

    13 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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