Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity Export

@article{citeulike:5077846, 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. 10.1074/mcp.M800512-MCP200}, author = {Sherman, Jamie and McKay, Matthew J. and Ashman, Keith and Molloy, Mark P.}, citeulike-article-id = {5077846}, citeulike-linkout-0 = {http://dx.doi.org/10.1074/mcp.M800512-MCP200}, citeulike-linkout-1 = {http://www.mcponline.org/content/8/9/2051.abstract}, citeulike-linkout-2 = {http://www.mcponline.org/content/8/9/2051.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19556279}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19556279}, day = {1}, doi = {10.1074/mcp.M800512-MCP200}, journal = {Mol Cell Proteomics}, keywords = {mrmaid, targeted\_proteomics}, month = {September}, number = {9}, pages = {2051--2062}, posted-at = {2009-11-04 19:38:33}, priority = {0}, title = {Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity}, url = {http://dx.doi.org/10.1074/mcp.M800512-MCP200}, volume = {8}, year = {2009} }

TY - JOUR ID - citeulike:5077846 L3 - citeulike-article-id:5077846 N2 - 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. 10.1074/mcp.M800512-MCP200 IS - 9 JF - Mol Cell Proteomics EP - 2062 TI - Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity VL - 8 SP - 2051 KW - mrmaid KW - targeted_proteomics AU - Sherman, Jamie AU - McKay, Matthew AU - Ashman, Keith AU - Molloy, Mark PY - 2009/09/01/ UR - http://dx.doi.org/10.1074/mcp.M800512-MCP200 ER -