We describe a method, filter-aided sample preparation (FASP), which combines the
advantages of in-gel and in-solution digestion for mass spectrometry–based proteomics. We
completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged
by urea on a standard filtration device. Peptides eluted after digestion on the filter were pure,
allowing single-run analyses of organelles and an unprecedented depth of proteome
coverage.