Our previous study found that high-molecular-weight selenium (Se) species make up 82% of the total Se in the bean of Se-enriched soybean plants (Chan et al. 2010, Metallomics, 2(2): p. 147-153). The Se species have been commonly seen in other plants in addition to soybean, but their identities remain unresolved. The present study employs a multi-technique metallomics approach to characterize the proteins containing Se in the beans of Se-enriched soybean plants. Two main categories of proteins, maturation proteins and protease inhibitors, were found in Se-containing high-performance liquid chromatography (HPLC) fractions. The proteins were screened by two-dimensional HPLC-inductively coupled plasma mass spectrometry, size-exclusion chromatography, and anion-exchange chromatography, and the Se-containing fractions were then identified by peptide mapping using HPLC-Chip-electrospray ion trap mass spectrometry. Based on the belief that Se goes into proteins through non-specific incorporation, a new method was designed and applied for the Se-containing peptide identification. The Se-containing peptide KSDQSSSYDDDEYSKPCCDLCMCTRS, part of the sequence of protein Bowman-Birk proteinase isoinhibitor (Glycine max), was found in one of the Se-containing fractions. The nutritional value of the Se-containing proteins in Se-enriched soybeans will be an interesting topic for the future studies.