Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species
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: li...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | Proteomes |
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| Online Access: | https://www.mdpi.com/2227-7382/9/4/46 |
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| author | Mário Jorge Araújo Maria Lígia Sousa Aldo Barreiro Felpeto Maria V. Turkina Elza Fonseca José Carlos Martins Vítor Vasconcelos Alexandre Campos |
| author_facet | Mário Jorge Araújo Maria Lígia Sousa Aldo Barreiro Felpeto Maria V. Turkina Elza Fonseca José Carlos Martins Vítor Vasconcelos Alexandre Campos |
| author_sort | Mário Jorge Araújo |
| collection | DOAJ |
| description | 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 <i>Scophthalmus maximus</i> and hepatopancreas of Mediterranean mussel <i>Mytilus galloprovincialis</i>. 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). |
| first_indexed | 2024-03-10T03:13:22Z |
| format | Article |
| id | doaj.art-2e8c415fd307490888f0a57d6e0e82f0 |
| institution | Directory Open Access Journal |
| issn | 2227-7382 |
| language | English |
| last_indexed | 2024-03-10T03:13:22Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Proteomes |
| spelling | doaj.art-2e8c415fd307490888f0a57d6e0e82f02023-11-23T10:20:05ZengMDPI AGProteomes2227-73822021-11-01944610.3390/proteomes9040046Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture SpeciesMário Jorge Araújo0Maria Lígia Sousa1Aldo Barreiro Felpeto2Maria V. Turkina3Elza Fonseca4José Carlos Martins5Vítor Vasconcelos6Alexandre Campos7CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalDepartment of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83 Linköping, SwedenCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalCIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, PortugalProteomics 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 <i>Scophthalmus maximus</i> and hepatopancreas of Mediterranean mussel <i>Mytilus galloprovincialis</i>. 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).https://www.mdpi.com/2227-7382/9/4/46aquaculture<i>Mytilus galloprovincialis</i><i>Scophthalmus maximus</i>protein profilingfunctional analysisFASP |
| spellingShingle | Mário Jorge Araújo Maria Lígia Sousa Aldo Barreiro Felpeto Maria V. Turkina Elza Fonseca José Carlos Martins Vítor Vasconcelos Alexandre Campos Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species Proteomes aquaculture <i>Mytilus galloprovincialis</i> <i>Scophthalmus maximus</i> protein profiling functional analysis FASP |
| title | Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species |
| title_full | Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species |
| title_fullStr | Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species |
| title_full_unstemmed | Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species |
| title_short | Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species |
| title_sort | comparison of sample preparation methods for shotgun proteomic studies in aquaculture species |
| topic | aquaculture <i>Mytilus galloprovincialis</i> <i>Scophthalmus maximus</i> protein profiling functional analysis FASP |
| url | https://www.mdpi.com/2227-7382/9/4/46 |
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