20140236497 | METHODS AND SYSTEMS FOR EXPERIMENTAL SET-UP AND DATA ANALYSIS IN TARGETED PROTEOMICS APPLICATIONS - The invention relates to the analysis of compounds with mass spectrometry and more particularly to instruments, substances, and methods for polypeptide analysis, in particular in targeted proteomics applications and based on indexed retention time as peptide specific property. The method of chemical analysis comprises the steps of: a) providing a first complex sample comprising a set of at least two reference peptides associated to an indexed retention time scale (iRT), as well as at least one further peptide; b) performing LC-MS on said complex sample and determining the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide; c) translating the empirical retention time values (RTe) of the reference peptides and of the at least one further peptide into the indexed retention time scale and associating to each reference peptide a reference indexed retention time value (iRTr) and to the at least one further peptide an associated indexed retention time value (iRTa); d) providing a second complex sample comprising at least one polypeptide as well as said set of the at least two reference peptides; e) performing LC-MS on said second complex sample and determining the empirical retention time values (RTe) of the reference peptides; f) translating the empirical retention time values (RTe) of the reference peptides into the indexed retention time scale by numerically adapting the transformation function for the conversion of the retention time values (RTe) into indexed retention time values such that the calculated indexed retention time values (iRTe) calculated based on the measured retention time values (RTe) of the reference peptides match the assigned indexed retention time values (iRTr) of the reference peptides; g) determining the predicted empirical retention time value (RTp) of the at least one further peptide by using the numerically adapted transformation function determined in step f). | 08-21-2014 |