Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics
Mass spectrometry-based proteomics relies on dedicated software for peptide and protein identification. These software include open-source or commercial-based search engines; wherein, they employ different algorithms to establish their scoring and identified proteins. Although previous comparative s...
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Elsevier
2021
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| Online Access: | http://psasir.upm.edu.my/id/eprint/96449/ https://www.sciencedirect.com/science/article/pii/S1874391921001391 |
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| author | Amir, Siti Hajar Mohd Yusof, Mohd Hafis Yuswan Wan Mohd Aizat Mansor, Muhammad Kamaruzaman Mohd Desa, Mohd Nasir Yusof, Yus Aniza Lai, Kok Song Mustafa, Shuhaimi |
| author_facet | Amir, Siti Hajar Mohd Yusof, Mohd Hafis Yuswan Wan Mohd Aizat Mansor, Muhammad Kamaruzaman Mohd Desa, Mohd Nasir Yusof, Yus Aniza Lai, Kok Song Mustafa, Shuhaimi |
| author_sort | Amir, Siti Hajar |
| building | UPM Library |
| collection | Institutional Repository |
| content_provider | Universiti Putra Malaysia |
| content_source | UPM Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | Mass spectrometry-based proteomics relies on dedicated software for peptide and protein identification. These software include open-source or commercial-based search engines; wherein, they employ different algorithms to establish their scoring and identified proteins. Although previous comparative studies have differentiated the proteomics results from different software, there are still yet studies specifically been conducted to compare and evaluate the search engine in the field of halal analysis. This is important because the halal analysis is often using commercial meat samples that have been subjected to various processing, further complicating its analysis. Thus, this study aimed to assess three open-source search engines (Comet, X! Tandem, and ProteinProspector) and a commercial-based search engine (ProteinPilot™) against 135 raw tandem mass spectrometry data files from 15 types of pork-based food products for halal analysis. Each database search engine contained high false-discovery rate (FDR); however, a post-searching algorithm called Peptide Prophet managed to reduce the FDR, except for Protein Prospector and Protein Pilot™. From this study, the combined database search engine (executed by iProphet) reveals a thorough protein list for pork-based food products; wherein the most abundant proteins are myofibrillar proteins. Thus, this proteomics study will aid the identification of potential peptide and protein biomarkers for future precision halal analysis. |
| format | Article |
| id | my.upm.eprints-96449 |
| institution | Universiti Putra Malaysia |
| publishDate | 2021 |
| publisher | Elsevier |
| record_format | eprints |
| spelling | my.upm.eprints-964492023-02-07T02:18:26Z http://psasir.upm.edu.my/id/eprint/96449/ Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics Amir, Siti Hajar Mohd Yusof, Mohd Hafis Yuswan Wan Mohd Aizat Mansor, Muhammad Kamaruzaman Mohd Desa, Mohd Nasir Yusof, Yus Aniza Lai, Kok Song Mustafa, Shuhaimi Mass spectrometry-based proteomics relies on dedicated software for peptide and protein identification. These software include open-source or commercial-based search engines; wherein, they employ different algorithms to establish their scoring and identified proteins. Although previous comparative studies have differentiated the proteomics results from different software, there are still yet studies specifically been conducted to compare and evaluate the search engine in the field of halal analysis. This is important because the halal analysis is often using commercial meat samples that have been subjected to various processing, further complicating its analysis. Thus, this study aimed to assess three open-source search engines (Comet, X! Tandem, and ProteinProspector) and a commercial-based search engine (ProteinPilot™) against 135 raw tandem mass spectrometry data files from 15 types of pork-based food products for halal analysis. Each database search engine contained high false-discovery rate (FDR); however, a post-searching algorithm called Peptide Prophet managed to reduce the FDR, except for Protein Prospector and Protein Pilot™. From this study, the combined database search engine (executed by iProphet) reveals a thorough protein list for pork-based food products; wherein the most abundant proteins are myofibrillar proteins. Thus, this proteomics study will aid the identification of potential peptide and protein biomarkers for future precision halal analysis. Elsevier 2021 Article PeerReviewed Amir, Siti Hajar and Mohd Yusof, Mohd Hafis Yuswan and Wan Mohd Aizat and Mansor, Muhammad Kamaruzaman and Mohd Desa, Mohd Nasir and Yusof, Yus Aniza and Lai, Kok Song and Mustafa, Shuhaimi (2021) Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics. Journal of Proteomics, 241. art. no. 104240. pp. 1-7. ISSN 1874-3919 https://www.sciencedirect.com/science/article/pii/S1874391921001391 10.1016/j.jprot.2021.104240 |
| spellingShingle | Amir, Siti Hajar Mohd Yusof, Mohd Hafis Yuswan Wan Mohd Aizat Mansor, Muhammad Kamaruzaman Mohd Desa, Mohd Nasir Yusof, Yus Aniza Lai, Kok Song Mustafa, Shuhaimi Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title | Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title_full | Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title_fullStr | Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title_full_unstemmed | Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title_short | Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| title_sort | comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics |
| url | http://psasir.upm.edu.my/id/eprint/96449/ https://www.sciencedirect.com/science/article/pii/S1874391921001391 |
| url_provider | http://psasir.upm.edu.my/ |