Discovery, identification, and informatics of low molecular weight peptide are extensively rising in the field of proteomics research. In this study, we analyzed protein profiles to discover peptide based biomarker for twelve different soybean seeds with three different agronomic types using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). For optimization of SELDI-TOF MS in soybean seed proteome analysis, four different extraction buffers were tested with urea solubilization buffer, thiourea/urea solubilization buffer, phenol extraction buffer, and modified trichloroacetic acid (TCA)/acetone precipitation/urea solubilization extraction buffer. Two different type of ProteinChip arrays, cation exchange (CM10) and anion exchange (Q10), applied to profile peptides. Among the four different extraction buffers, phenol extraction was selected to protein extraction methodology. Numbers of detected peak cluster in twelve soybean seeds were 125 at CM10 and 90 at Q10 array in the mass range from 2 to 40 kDa. Among them, 82 peak clusters at CM10 and 33 peak clusters at Q10 array showed significantly different peak clusters at p<0.00004 (CM10) and p<0.00005 (Q10) among twelve different soybean cultivars. Moreover, 29 peak clusters at CM10 and 17 peak clusters at Q10 array were detected in all cultivars as an ‘universally existed peptide’. In comparison with three different agronomic types, total of 55 peak clusters (CM10) and 23 peak clusters (Q10) were significantly different peak clusters at p<0.00004 and p<0.0001, respectively. In these probability levels, soybean seeds were well discriminated into different cultivar and different type with each other. Also we could find several specific peptide biomarkers for agronomic type.

Developmental changes of chlorophyll-protein complexes (CPs) and plastid membrane proteins in greening mung bean cotyledons and the effect of spermine thereon were examined by SDS-polyacrylamide gel electrophoresis. The changes in the amounts of CPs became larger with the progress of greening and light-harvesting chlorophyll a/b protein (LHCP) was the main CP in the early greening stage up to 48 h. As the greening proceeded, chlorophyll-protein of the photosystem I (CPI) accumulated. Application of spermine were effective in accumulating CPs of the thylakoid membrane in the early phase of greening. In the profiles of the plastid membrane proteins, quantitative and qualitative changes were observed with the onset of greening up to 72 h. 56 kD protein of major intensity was observed in all greened chloroplasts and 24 kD protein increased remarkablly in both control and spermine-treated cotyledons. The thylakoids from spermine-treated cotyledons showed higher amounts of thylakoid proteins as compared to the controls. The results suggest that spermine may play a role in the regulation of plastid development and stabilizes the membrane function during greening.