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

Araujo, Mario Jorge (author)
Univ Porto, Portugal
Sousa, Maria Ligia (author)
Univ Porto, Portugal
Felpeto, Aldo Barreiro (author)
Univ Porto, Portugal
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Turkina, Maria V, 1973- (author)
Linköpings universitet,Avdelningen för neurobiologi,Medicinska fakulteten
Fonseca, Elza (author)
Univ Porto, Portugal
Martins, Jose Carlos (author)
Univ Porto, Portugal
Vasconcelos, Vitor (author)
Univ Porto, Portugal; Univ Porto, Portugal
Campos, Alexandre (author)
Univ Porto, Portugal
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 (creator_code:org_t)
2021-11-16
2021
English.
In: Proteomes. - : MDPI. - 2227-7382. ; 9:4
Related links:
https://liu.diva-por... (primary) (Raw object)
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https://doi.org/10.3...
https://urn.kb.se/re...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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).

Subject headings

NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

Keyword

aquaculture; Mytilus galloprovincialis; Scophthalmus maximus; protein profiling; functional analysis; FASP; SP3; S-Trap

Publication and Content Type

ref (subject category)
art (subject category)

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