Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species

• Type: Article in International Scientific Journal
• Date: 2021

Authors

Maria J Araujo (Author) FCUP; Sousa, ML (Author) Other; Felpeto, AB (Author) Other; Turkina, MV (Author) Other; Fonseca, E (Author) Other; Martins, JC (Author) Other; Vitor Vasconcelos (Author) FCUP; Alexandre Campos (Author) FCUP

Journal

Title: Proteomes

Vol. 9

Publisher: MDPI

Indexing

ISI Web of Knowledge - 5 Citations

Scopus - 5 Citations

Other information

Authenticus ID: P-00V-QAV

DOI: 10.3390/proteomes9040046

Abstract (EN): Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC-MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 19