In this work, a novel approach based on off-line coupling of a single run of capillary electrophoresis (CE) separation to both matrix-assisted laser desorption/ionization (MALDI) and substrate-assisted laser desorption inductively coupled plasma (SALD ICP) mass spectrometry (MS) is presented. Using a liquid junction and subatmospheric deposition chamber, CE fractions were extracted from a separation capillary and collected as 20-nL droplets on a custom-built polyethylene terephthalate glycol (PETG) target plate coated with a 10-nm gold layer which guaranteed compatibility with both MALDI and SALD ICP techniques. The MALDI matrix solution was then added to the produced spots. After it was dried, the separation record was consecutively analyzed in MALDI MS and ICP MS instruments. Thus, both proteomic and metallomic information was obtained off-line from a single CE run. The concept was demonstrated by the analysis of a mixture of rabbit liver metallothionein isoforms. In an additional study, the droplets representing the archived separation record were alternately mixed with two different MALDI matrices to obtain complementary information on both the apoproteins and their complexes with metals from a single separation run. The presented technique is a viable alternative to online coupling of column separation to electrospray MS and nebulizer ICP MS.