The invention provides a high-throughput method for quantitating plant seed proteins, e.g. seed allergens. Such method involves obtaining a protein sample from the seed; analyzing the sample using mass spectrometry with a set of pre-designed internal standard peptides that are specific to the plant allergens; and monitoring frequencies and intensities of resulting spectra to obtain relative and absolute allergen contents in the seed. The invention also provides a system for high-throughput profiling of plant seed allergens. Such system comprises a set of pre-designed internal standard peptides that are specific to the plant seed allergens and one or more mass spectrometers.