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We have optimized a protocol to separate condensates from cells using chemical cross\u2010linking followed by size\u2010exclusion chromatography (SEC). After SEC fractionation, the samples can be characterized by a variety of approaches including enzyme\u2010linked immunosorbent assay, dynamic light scattering, electron microscopy, and mass spectrometry. The protocol described here has been optimized for cultured mammalian cells and <jats:italic>E. coli<\/jats:italic> expressing recombinant proteins. Since the lysates are fractionated by size, this protocol can be modified to study other large protein assemblies, including the nuclear pore complex, and for other tissues or organisms. \u00a9 2021 Wiley Periodicals LLC.<\/jats:p><jats:p>This article was corrected on 20 July 2022. See the end of the full text for details.<\/jats:p><jats:p><jats:bold>Basic Protocol 1<\/jats:bold>: SEC separation of cross\u2010linked mammalian cell lysates<\/jats:p><jats:p><jats:bold>Alternate Protocol<\/jats:bold>: Preparation of non\u2010crosslinked mammalian cells<\/jats:p><jats:p><jats:bold>Basic Protocol 2<\/jats:bold>: SEC separation of <jats:italic>E. coli<\/jats:italic> lysate<\/jats:p><jats:p><jats:bold>Support Protocol 1<\/jats:bold>: Detecting protein of interest by ELISA<\/jats:p><jats:p><jats:bold>Support Protocol 2<\/jats:bold>: TCA precipitation of SEC fractions<\/jats:p>","DOI":"10.1002\/cpz1.35","type":"journal-article","created":{"date-parts":[[2021,3,19]],"date-time":"2021-03-19T18:29:38Z","timestamp":1616178578000},"source":"Crossref","is-referenced-by-count":13,"title":["Isolating and Analyzing Protein Containing Granules from Cells"],"prefix":"10.1002","volume":"1","author":[{"given":"Rachel 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