Can proteins from unsequenced organisms be identified by mass spectrometry?
Protein identification is based on searching against either public databases such as NCBInr or against databases created from protein sequences provided by investigators. Therefore, if the genomic or protein sequence is not known, we will be unable to identify the protein using bioinformatics. Only in instances for which there is considerable homology between groups of organisms it may be possible to identify proteins based on the few peptides that are identical to those of a known protein sequence. Alternatively, one could identify the sequence of an unknown peptide by “de-novo sequencing”. However, this method is operator driven and as such is not well suited for high throughput proteomics.
