A method of chemical LC-SWATH (Liquid Chromatography - Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) analysis, comprising; a) providing a first complex sample comprising a set of at least five 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) measured in step b) of the reference peptides and of the at least one further peptide in a first translation by a transformation function 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 peptide as well as said set of the at least five 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) measured in step e) of the reference peptides in a second translation by said transformation function into the indexed retention time scale by numerically adapting said transformation function (RTe = f(iRTr)) for the translation of the retention time values (RTe) measured in step e) into indexed retention time values such that the calculated indexed retention time values (iRTe) calculated based on the measured retention time values (RTe) measured in step e) 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 (RTp = f(iRTa)) determined in step f), wherein in step e) an LC tandem mass spectroscopy in the form of LC-SWATH is used and wherein said predicted empirical retention time value (RTp) is used for corresponding selective data analysis of data slices characterizing the further peptide. a) providing a first complex sample comprising a set of at least five 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) measured in step b) of the reference peptides and of the at least one further peptide in a first translation by a transformation function 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 peptide as well as said set of the at least five 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) measured in step e) of the reference peptides in a second translation by said transformation function into the indexed retention time scale by numerically adapting said transformation function (RTe = f(iRTr)) for the translation of the retention time values (RTe) measured in step e) into indexed retention time values such that the calculated indexed retention time values (iRTe) calculated based on the measured retention time values (RTe) measured in step e) 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 (RTp = f(iRTa)) determined in step f),