Title

Protein Identification and Quantification from Riverbank Grape, Vitis riparia: Comparing SDS‐PAGE and FASP‐GPF Techniques for Shotgun Proteomic Analysis

Document Type

Article

Publication Date

2015

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 FASPGPF 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).

Publication Title

Proteomics

Volume

15

First Page

3061

Last Page

3065

DOI of Published Version

10.1002/pmic.201500085

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