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

Abstract

The growing use of selected reaction monitoring (SRM) mass spectrometry in proteomic analyses led us to investigate how to identify peptides by SRM using only a minimal 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 using a modified SRM methodology to profile the E. coli tricarboxylic acid cycle from a single injection of cell lysate. In addition, we showed the potential of UIS to form the first functionally orthogonal approach to validate peptide assignments obtained from conventional analyses of MS/MS spectra. The UIS methodology is a novel deterministic peptide identification method for MS/MS spectra based on information content. These robust theoretical assays will have widespread use when integrated with previously collected MS/MS data and conventional proteomics technologies. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.