Identification of Peptide Biomarkers for Discrimination of Shrimp Species through SWATH-MS-Based Proteomics and Chemometrics

Abstract

Incorrect labeling and adulteration of shrimp occurs due to interspecies similarities and carapace removal during processing. This study attempted to identify three related commercial shrimp species of the order Decapoda: Marsupenaeus japonicus, Fenneropenaeus chinensis, and Litopenaeus vannamei. All measurable trypsin-digested peptides in the individual shrimp were detected using ultrahigh-performance liquid chromatography quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition. Further analysis of peptide biomarkers was carried out with an orthogonal partial least-squares discriminant analysis (OPLS-DA) model. BLAST was used for species-specific analysis. Subsequently, multiple reaction monitoring (MRM) methods were developed for sensitivity and selectivity screening of the selected peptides, and 27 were identified as biomarkers allowing rapid and accurate discrimination of shrimp species without high-resolution mass spectrometry or statistical model building. These strategies could be applied in authentication of other products containing highly homologous proteomes.

Label-Free Quantitative Proteomics Reveals the Multitargeted Antibacterial Mechanisms of Lactobionic Acid against Methicillin-Resistant Staphylococcus aureus (MRSA) using SWATH-MS Technology

“…Comparative quantitation of proteomes has become a useful approach to underlying the mechanism of antimicrobial agents by detecting the differential abundance of proteins. Sequential window acquisition of all theoretical mass spectra (SWATH-MS), a recently developed label-free quantitative proteomics method that can quantify several thousand proteins in parallel, has been used for biomarker discovery and bacterial responses to stress because of its higher sensitivity and accuracy . In addition, parallel reaction monitoring (PRM)-based targeted mass spectrometry, which has high sensitivity and selectivity, has emerged as an alternative method for targeted protein quantification.…”

Integration of Untargeted and Pseudotargeted Metabolomics for Authentication of Three Shrimp Species Using UHPLC-Q-Orbitrap

“…This fact, coupled with the severe price disparities in shrimps of different species, gives rise to a high risk of food fraud. Species identity is one of the most valued food authenticity attributes for fishery and aquaculture products, and authentication of shrimp from different species has already become a growing global concern …”

Comparison of the effectiveness of variable selection method for creating a diagnostic panel of biomarkers for mass spectrometric lipidome analysis

“…Variable importance in projection (VIP) is used in OPLS‐DA for feature selection where VIP var , SS var , pred , SS var , p var —VIP, sum of squares explained part, common sum of squares, and loading score of the independent variable var , respectively; SS y , pred , SS y , q—sum of squares explained part, common sum of squares, and loading score of response variable, respectively; and K —common number of variables 6 . The VIP threshold, used in many cases to identify a variable as a discrimination marker, is VIP > 1 7,8 …”

“…6 The VIP threshold, used in many cases to identify a variable as a discrimination marker, is VIP > 1. 7,8 Random forest (RF) is a method based on the construction of several hundred "decision trees" for classification. It is based on the limited size of a set of variables.…”