Identification of Species-Specific Peptide Markers in Highly Processed Meat Products Using De Novo Sequencing
peer-reviewed · Foods · 2026
| Date | 2026-06-26 |
| Type | peer-reviewed |
| Venue | Foods |
| Publisher | MDPI |
| Contribution | downstream-application |
| DOI | 10.3390/foods15132294 |
| Citations (OpenAlex) | 0 |
Abstract
Processed meat products represent a major challenge for proteomic species identification due to extensive thermal treatment and protein structural changes. In this study, species-specific peptides in pork, chicken, and bovine meat products were identified using a directed fragmentation-assisted de novo sequencing workflow that combines 4-formylbenzene-1,3-disulfonic acid (FBDA) peptide derivatization, dual-polarity data-independent mass spectrometry (DIA-MS), and Protein Acrobat de novo sequencing software. Comparative analysis of non-fractionated and strong cation exchange (SCX)-fractionated pork luncheon samples improved peptide and protein identification after fractionation, with 312 peptides and 115 protein groups detected exclusively in fractionated samples. Species-specific peptides were predominantly assigned to conserved muscle-related proteins, including myosin, troponin, and tropomyosin, while sequence variability enabled reliable species discrimination despite protein conservation across species. To evaluate applicability for food fraud detection, mixed meat samples containing 10% chicken in pork or bovine matrices were analyzed, reflecting potential economically motivated adulteration through substitution with lower-cost meat components. Several chicken-specific peptides remained detectable in both mixtures, demonstrating robustness of the FBDA-assisted peptide sequencing combined with SCX fractionation and DIA-MS for detection of adulteration in complex processed food matrices. These findings establish a mass spectrometry-driven orthogonal method to ELISA testing for fast, reliable and accurate metaproteome analysis of highly processed food.
Methods and tools
- Processed meat species markers: De novo peptide sequencing workflow combining FBDA peptide derivatization, dual-polarity DIA-MS, and SCX fractionation to discover species-specific markers (myosin, troponin) in highly processed pork, chicken and bovine meat products, enabling detection of adulteration down to 10 % species contamination.
- Protein Acrobat: De novo peptide sequencing tool from the Cindrić group, coupling MALDI-TOF/TOF fragmentation of chemically activated peptides with de novo sequence elucidation and NCBInr alignment for organism identification (bacteria, viruses, meat-species markers).
Cites (4)
- A transformer model for de novo sequencing of data independent acquisition mass spectrometry data (2025) crossref
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023) crossref
- Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing (2022) crossref
- Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets (2016) crossref