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Two-dimensional gel electrophoresis was used to screen spring barley cultivars for differences in seed protein profiles. In parallel, 72 microsatellite (simple sequence repeat (SSR)) markers and 11 malting quality parameters were analysed for each cultivar. Over 60 protein spots displayed cultivar variation, including peroxidases, serpins and proteins with unknown functions. Cultivars were clustered based on the spot variation matrix. Cultivars with superior malting quality grouped together, indicating malting quality to be more closely correlated with seed proteomes than with SSR profiles. Mass spectrometry showed that some spot variations were caused by amino acid differences encoded by single nucleotide polymorphisms (SNPs). Coding SNPs were validated by mass spectrometry, expressed sequence tag and 2D gel data. Coding SNPs can alter function of affected proteins and may thus represent a link between cultivar traits, proteome and genome. Proteome analysis of doubled haploid lines derived from a cross between a malting (Scarlett) and a feed cultivar (Meltan) enabled genetic localisation of protein phenotypes represented by 48 spot variations, involving e.g. peroxidases, serpins, α-amylase/trypsin inhibitors, peroxiredoxin and a small heat shock protein, in relation to markers on the chromosome map.

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