title: Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification.
abstract: Timely classification and identification of bacteria is of vital importance in many areas of public health. We present a mass spectrometry (MS)-based proteomics approach for bacterial classification. In this method, a bacterial proteome database is derived from all potential protein coding open reading frames (ORFs) found in 170 fully sequenced bacterial genomes. Amino acid sequences of tryptic peptides obtained by LC-ESI MS/MS analysis of the digest of bacterial cell extracts are assigned to individual bacterial proteomes in the database. Phylogenetic profiles of these peptides are used to create a matrix of sequence-to-bacterium assignments. These matrixes, viewed as specific assignment bitmaps, are analyzed using statistical tools to reveal the relatedness between a test bacterial sample and the microorganism database. It is shown that, if a sufficient amount of sequence information is obtained from the MS/MS experiments, a bacterial sample can be classified to a strain level by using this proteomics method, leading to its positive identification.
authors.affiliation: Geo-Centers, Inc., Aberdeen Proving Ground, Maryland 21010-0068, USA. jacek.dworzanski@us.army.mil
authors.forename: Jacek P
authors.initials: JP
authors.lastname: Dworzanski
authors.forename: Samir V
authors.initials: SV
authors.lastname: Deshpande
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Rabih E
authors.initials: RE
authors.lastname: Jabbour
authors.forename: A Peter
authors.initials: AP
authors.lastname: Snyder
authors.forename: Charles H
authors.initials: CH
authors.lastname: Wick
authors.forename: Liang
authors.initials: L
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000145:classification*; D001426:Bacterial Proteins / Q000032:analysis*; D019295:Computational Biology; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis; D010449:Peptide Mapping; D010802:Phylogeny; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D010446:Peptide Fragments; D020543:Proteome