title: A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation.
abstract: Shotgun proteomics is an emerging tool for bacterial identification and differentiation. However, the identification of the mass spectra of peptides to genome-derived peptide sequences remains a key issue that limits the use of shotgun proteomics to bacteria with genome sequences available. In this proof-of-concept study, we report a novel bacterial fingerprinting method that enjoys the resolving power and accuracy of mass spectrometry without the burden of peptide identification (i.e. genome sequence-independent). This method uses a similarity-clustering algorithm to search for mass spectra that are derived from the same peptide and merge them into a unique consensus spectrum as the basis to generate proteomic fingerprints of bacterial isolates. In comparison to a traditional peptide identification-based shotgun proteomics workflow and a PCR-based DNA fingerprinting method targeting the repetitive extragenic palindromes elements in bacterial genomes, the novel method generated fingerprints that were richer in information and more discriminative in differentiating E. coli isolates by their animal sources. The novel method is readily deployable to any cultivable bacteria, and may be used for several fields of study such as environmental microbiology, applied microbiology, and clinical microbiology.
authors.affiliation: Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Wenguang
authors.initials: W
authors.lastname: Shao
authors.affiliation: Division of Environment, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.|Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.affiliation: Division of Environment, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.|Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Stanley C K
authors.initials: SC
authors.lastname: Lau
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002853:Chromatography, Liquid / Q000379:methods; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005243:Feces / Q000382:microbiology; D058889:Molecular Typing / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D040901:Proteomics / Q000379:methods; D017422:Sequence Analysis, DNA; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D004269:DNA, Bacterial