Classification and identification of bacteria using mass spectrometry-based proteomics

Abstract

Timely classification and identification of bacteria is of vital importance in many areas of public health. Mass spectrometry-based methods provide an attractive alternative to well-established microbiologic procedures. Mass spectrometry methods can be characterized by the relatively high speed of acquiring taxonomically relevant information. Gel-free mass spectrometry proteomics techniques allow for rapid fingerprinting of bacterial proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or, for high-throughput sequencing of peptides from protease-digested cellular proteins, using mass analysis of fragments from collision-induced dissociation of peptide ions. The latter technique uses database searching of product ion mass spectra. A database contains a comprehensive list of protein sequences translated from protein-encoding open reading frames found in bacterial genomes. The results of such searches allow the assignment of experimental peptide sequences to matching theoretical bacterial proteomes. Phylogenetic profiles of sequenced peptides are then used to create a matrix of sequence-to-bacterium assignments, which are analyzed using numerical taxonomy tools. The results thereof reveal the relatedness between bacteria, and allow the taxonomic position of an investigated strain to be inferred.

Highly Efficient Classification and Identification of Human Pathogenic Bacteria by MALDI-TOF MS

“…Both of the approaches demonstrated the accuracy of bacterial classification and identification in two independently prepared sets of bacterial isolates (containing 37 and 38 isolates, respectively). Indeed application of MALDI-TOF MS for rapid bacterial identification has been reported before (7,23,24,39,40). A database of more than 3500 MALDI-TOF MS spectra with multiple bacterial strain entries from most bacterial species has been established and used for a rapid screening and characterization of bacteria implicated in human diseases using spectrum fingerprinting analysis.…”

“…MS with its capability of de novo protein/peptide sequencing (such as electrospray ionization or MALDI-TOF MS for tandem MS/MS) or its high efficiency for proteome profiling (particularly MALDI-TOF MS) has been suggested as an alternative for microbial identification (2)(3)(4)(5)(6)(7). In the past decade, extraction of bacterial proteins for sequencing using tandem MS/MS (8 -11) or for proteome profiling followed by matching MS spectrum results to databases (fingerprinting) have been used for bacterial identification (6,8,(12)(13)(14)(15).…”

Systematics, Taxonomy and Classification of Bacteria

“…Филогенети-ческими маркерами служат рРНК, в первую очередь -16S-рРНК, а взаимоотношения ор-ганизмов наглядно изображают графически в виде филогенетических деревьев [1,2,3,4,5,6].…”

Comparison of peptide cancer signatures identified by mass spectrometry in serum of patients with head and neck, lung and colorectal cancers: Association with tumor progression

“…In this approach specific proteome signatures are built based on several peptide/protein components, which can be exemplified by ions registered at defined m/z values in the mass spectrum. Such signatures can be used for sample identification and classification even though their particular components may lack differentiating power when analyzed separately (6)(7)(8)(9). Matrix-assisted laser desorption/ionization spectrometry (MALDI), and its derivative surface-enhanced laser desorption/ ionization spectrometry (SELDI), coupled to a time-of-flight (ToF) type of analyzers, appear to be particularly suitable for such proteome pattern analysis.…”