RMIDb: Rapid Microorganism Identification Database

NOTE: (July 12th, 2010) The RMIDb is currently being updated and its relational databases being rebuilt. We are making every effort to do this as quickly and efficiently as possible. If you would like to be notified when the RMIDb is back up and running, please contact Nathan Edwards (nje5@georgetown.edu). Thanks for your patience! -n

Rapid Microorganism Identification Database (RMIDb)

Use this database to identify bacteria and viruses using existing mass spectrometry protocols, and to develop new experimental protocols for microorganism identification by mass spectrometry.

The RMIDb contains all bacterial, virus, plasmid, and environmental protein sequences from the Ventor Institute's Comprehensive Microbial Resource (CMR), UniProt's Swiss-Prot and TrEMBL, Genbank's Protein, and RefSeq's Protein and Genome. In addition, Glimmer3 has been used to predict an agressive set of putative proteins, including alternative translation start-sites, on all RefSeq bacterial genomes.

The RMIDb currently supports both intact protein and peptide based rapid identification protocols. Trypsin and acid-based cleavage protocols are currently available. The Pfam protein family and Gene Onotolgy protein classifications are also provided, so that the experimenatally likely proteins can be preferentially searched.

The RMIDb provides tools for the in silico study of proteins and peptides as a source of potential species biomarkers, providing searches for unique and shared markers by mass and sequence.

The RMIDb uses sophisticated statistical significance models to determine the likelihood that the masses observed in a mass spectrum match the theoretical masses of a species' proteins by chance. If a chance match is sufficiently unlikely, the identity of the organism is established. Unlike previous approaches, the RMIDb need make no assumptions about the uniformity of protein or peptide masses across the mass range or the independence of random matches to different input masses.

Problems, questions, comments? Contact Nathan Edwards.

Recent references using the RMIDb

1. C. Fenselau, S. Russell, S. Swatkoski, and N. Edwards. European Journal of Mass Spectrometry (2007). Proteomic Strategies for Rapid Analysis of Microorganisms.
2. S.C. Russell, N. Edwards, and C. Fenselau. Anal. Chem. (2007) Detection of Plasmid Insertion in Escherichia coli by MALDI-TOF Mass Spectrometry.
3. N.J. Edwards and F. Pineda. Poster at ASMS (2006) Rapid Microorganism Identification Database (www.RMIDb.org).
4. S. Swatkoski, S.C. Russell, N. Edwards, and C. Fenselau. Anal. Chem. (2006) Rapid Chemical Digestion of Small Acid-Soluble Spore Proteins for Analysis of Bacillus Spores.

1. F. J. Pineda, M. D. Antoine, P. A. Demirev, A. B. Feldman, J. Jackman, M. Longenecker and J. S. Lin, Anal. Chem (2003) Microorganism Identification by Matrix-Assisted Laser/Desorption Ionization Mass Spectrometry and Model-Derived Ribosomal Protein Biomarkers
2. F. Pineda, ASM BioDefense Research Meeting, Mar. 9-12, 2003, Baltimore MD, A Database for MALDI-MS Rapid microorganism Identification
3. P.Demirev, F. Pineda, J.Lin, C.Fenselau, Anal.Chem 73 (2001), 4566-4573, Bioinformatics and mass spectrometry for microorganism identification: Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori.
4. F. Pineda, J.Lin, C.Fenselau, P.Demirev, Anal.Chem. 72 (2000), 3739-3744, A model for significance testing of proteome database search algorithms in microorganism identification.
5. P.Demirev, Y.P.Ho, V.Ryzhov, C.Fenselau, Anal.Chem. 71 (1999), 2732-2738, Microorganism identification by mass spectrometry and protein database searches.

1. C.Fenselau, P.Demirev, Mass Spectrometry Reviews 20 (2001), 157-171, Characterization of intact microorganisms by MALDI mass spectrometry.