The generation of retention index (RI) libraries is an expensive and time-consuming effort. Procedures for the transfer of RI properties between chromatography variants are, therefore, highly relevant for a shared use. The precision of RI determination and accuracy of RI transfer between 8 method variants employing 5%-phenyl-95%-dimethylpolysiloxane capillary columns was investigated using a series of 9 n-alkanes (C(10)-C(36)). The precision of the RI determination of 13 exemplary fatty acid methyl esters (C(8) ME-C(30) ME) was 0.22-0.33 standard deviation (S.D.) expressed in RI units in low complexity samples. In the presence of complex biological matrices this precision may deteriorate to 0.75-1.11. Application of the previously proposed Kováts, van den Dool or 3rd-5th order polynomial regression algorithms resulted in similar precision of RI calculation. For transfer of empirical van den Dool-RI properties between the chromatography variants 3rd order regression was found to represent the minimal necessary assumption. The range of typical regression coefficients was r(2)=0.9988-0.9998 and accuracy of RI prediction between chromatography variants varied between 5.1 and 19.8 (0.29-0.69%) S.D. of residual RI error, RI(predicted)-RI(determined) (n>64). Accuracy of prediction was enhanced when subsets of chemically similar compound classes were used for regression, for example organic acids and sugars exhibited 0.78 (n=29) and 3.74 (n=37) S.D. of residual RI error, respectively. In conclusion, we suggest use of percent RI error rather than absolute RI units for the definition of matching thresholds. Thresholds of 0.5-1.0% may apply to most transfers between chromatography variants. These thresholds will not solve all matching ambiguities in complex samples. Therefore, we recommend co-analysis of reference substances with each GC-MS profiling experiment. Composition of these defined reference mixtures may best approximate or mimic the quantitative and qualitative composition of the biological matrix under investigation.