Identification of mouse brain proteoforms: comparison of 2D-electrophoresis data and independent experiment with mass spectrometric identification.

Abstract

A previously developed algorithm for the preliminary identification of protein proteoforms associated with post-translational modifications (PTMs) based on 2D electrophoresis data (DOI: 10.18097/BMCRM00191) has been used in this study for analysis of experimental data obtained using mice and reported in two papers by different authors. The authors of the first paper identified 8 groups of spots on 2D electrophoretic maps corresponding to 8 proteins with at least two unconcretised proteoforms. The authors of the second paper analyzed brain samples by means of the LC-MS/MS. In this study identification of peptides with PTMs was repeated using the raw data from the second paper. Among the 8 target proteins, 7 were identified in most of the biological samples. For 4 of them, 17 possible peptides with modifications were found. The 5 proteoform variants with identified PTMs matched the spots on the 2D electrophoresis maps. Thus, the prediction of pI values for proteins with hypothetical PTMs allows to form a set of hypotheses about the presence of particular proteoforms on the 2D electrophoretic maps.