A robust protocol for protein extraction and digestion

Michelle Atallah, Mark R. Flory, Parag Mallick

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations


Proteins play a key role in all aspects of cellular homeostasis. Proteomics, the large-scale study of proteins, provides in-depth data on protein properties, including abundances and post-translational modification states, and as such provides a rich avenue for the investigation of biological and disease processes. While proteomic tools such as mass spectrometry have enabled exquisitely sensitive sample analysis, sample preparation remains a critical unstandardized variable that can have a significant impact on downstream data readouts. Consistency in sample preparation and handling is therefore paramount in the collection and analysis of proteomic data. Here we describe methods for performing protein extraction from cell culture or tissues, digesting the isolated protein into peptides via in-solution enzymatic digest, and peptide cleanup with final preparations for analysis via liquid chromatography-mass spectrometry. These protocols have been optimized and standardized for maximum consistency and maintenance of sample integrity.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages10
StatePublished - 2017
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Acetone precipitation
  • Enzymatic solution digest
  • Liquid chromatography-mass spectrometry
  • Protein extraction
  • Proteomics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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