Methods and systems for experimental set-up and data analysis in targeted proteomics applications

A method of chemical analysis, comprising;

• a) providing a first complex sample comprising a set of at least two reference peptides associated to an indexed retention time scale, as well as at least one further peptide,
• b) performing LC-MS on said complex sample and determining empirical retention time values RTe of the reference peptides and of the at least one further peptide,
• c) translating said 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 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 f
• RTe=f(iRTr)
• for the conversion of the retention time values RTe into indexed retention time values such that the calculated indexed retention time values RTe calculated based on the measured retention time values RTe of the reference peptides optimally 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 f determined in step f) as follows:
• RTp=f(iRTa)
• wherein the predicted empirical retention time value (RTp) is used for at least one of the following:
• the identification of the corresponding further peptide;
• the determination of a retention time window for the corresponding further peptide;
• and, the definition of one or more regions where the further peptide cannot occur.