Unique ion signature mass spectrometry, a deterministic method to assign peptide identity

The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to inves-tigate how to identify peptides by SRM using only a min-imal number of fragment ions. By using a computational model of the SRM work flow we computed the potential interferences from other peptides in a given proteome. From these results, we selected the deterministic SRM addresses that contained sufficient information to confer peptide and protein identity that we termed unique ion signatures (UIS). We computationally showed that UIS comprised of only two transitions are diagnostic for>99 % of Escherichia coli proteins and>96 % of human proteins that possess a sequence-unique peptide. We demonstrated an example of experimental use of UIS us-ing a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell ly