Membrane protein identifications by mass spectrometry using electrocapture-based separation as part of a two-dimensional fractionation system

A two-dimensional (2D) separation method was used to decrease sample complexity in analysis of tryptic peptides from glomerular membrane proteins by tandem mass spectrometry (MS/MS). The first dimension was carried out by electrocapture (EC), which fractionates peptides according to electrophoretic mobility. The second dimension was reverse-phase liquid chromatography (RP-LC), in which EC fractions were further separated and analyzed online by MS/MS. Using this methodology, we now identify 102 glomerular proteins (57 membrane proteins). Many peptides were possible to observe and select for MS/MS only using the 2D approach. Others were detectable in both one-dimensional (I D, without the EC step) and 2D experiments but were selectable for sequence analysis only from the 2D separations because the decrease in complexity then gives time for the mass analyzer to select the peptide and switch to the MS/ MS mode. A minority of the peptides were detectable only in the I D mode (presumably because of handling losses), but at the end this did not decrease the number of proteins identified by the 2D separation. After a database search, the combination of EC and RP-LC MS/MS versus a I D RP-LC MS/MS separation resulted in a threefold increase in the number of proteins identified and improved the sequence coverage in the identifications, bringing our proteome-identified glomerular proteins to 282. (c) 2008 Elsevier Inc. All rights reserved.