Mass spectrometry-based proteomics combined with bioinformatic tools for bacterial classification |
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Authors: | Dworzanski Jacek P Deshpande Samir V Chen Rui Jabbour Rabih E Snyder A Peter Wick Charles H Li Liang |
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Institution: | Geo-Centers, Inc., Aberdeen Proving Ground, Maryland 21010-0068, USA. jacek.dworzanski@us.army.mil |
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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. |
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