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.
In all, 30,559,885 protein sequences (15,175,216 distinct protein sequences) from 55,656 organisms representing 24,304 species are available for searching.
The RMIDb has protein sequences from 732 complete genomes representing 523 species.
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