UPM Institutional Repository

Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics


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


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.

Download File

Full text not available from this repository.

Additional Metadata

Item Type: Article
Divisions: Faculty of Biotechnology and Biomolecular Sciences
Faculty of Engineering
Faculty of Medicine and Health Science
Halal Products Research Institute
DOI Number: https://doi.org/10.1016/j.jprot.2021.104240
Publisher: Elsevier
Keywords: Proteomics; Database; Search engines; Halal; Pork
Depositing User: Ms. Nuraida Ibrahim
Date Deposited: 07 Feb 2023 02:18
Last Modified: 07 Feb 2023 02:18
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.1016/j.jprot.2021.104240
URI: http://psasir.upm.edu.my/id/eprint/96449
Statistic Details: View Download Statistic

Actions (login required)

View Item View Item