Chromatographic behaviour of peptides following dimethylation with H2/D2-formaldehyde: Implications for comparative proteomics

The differential separation of deuterated and non-deuterated forms of isotopically substituted compounds in chromatography is a well-known but not well-understood phenomenon. This separation is relevant in comparative proteomics, where stable isotopes are used for differential labelling and the effect of isotope resolution on quantitation has been used to disqualify some deuterium labelling methods in favour of heavier isotopes. In this work, a detailed evaluation of the extent of isotopic separation and its impact on quantitation was performed for peptides labelled through dimethylation with H2/D2 formaldehyde. The chromatographic behaviour of 71 labelled peptide pairs from quadruplicate tryptic digests of bovine serum albumin were analysed, focusing on differences in median retention times, resolution, and relative quantitation for each peptide. For 94% of peptides, the retention time difference (heavy-light) was less than 12 s with a median value 3.4 s. With the exception of a single anomalous pair, isotope resolution was below 0.6 with a median value 0.11. Quantitative assessment indicates that the bias in ratio calculation introduced by retention time shifts is only about 3%, substantially smaller than the variation in ratio measurements themselves. Computational studies on the dipole moments of deuterated labels indicate that these results are consistent with literature suggestions that retention time shifts are inversely related to the polarity of the label. This study suggests that the incorporation of deuterium isotopes through peptide dimethylation at amine residues is a viable route to proteome quantitation.

► The isotope effect (D0 vs D4) in dimethyl labelling of peptide pairs is examined. ► Four replicates of 71 peptide pairs are used to assess retention time differences. ► Retention differences are statistically significant, but small and inconsequential. ► Computational results are consistent with observations for other labelling methods. ► Dimethyl labelling is a viable alternative for relative peptide quantitation.