Quantitative analysis of global protein lysine methylation by mass spectrometry

Peder J. Lund, Stephanie M. Lehman, Benjamin A. Garcia

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

10 Scopus citations


Since protein activity is often regulated by posttranslational modifications, the qualitative and quantitative analysis of modification sites is critical for understanding the regulation of biological pathways that control cell function and phenotype. Methylation constitutes one of the many types of posttranslational modifications that target lysine residues. Although lysine methylation is perhaps most commonly associated with histone proteins and the epigenetic regulation of processes involving chromatin, methylation has also been observed as an important regulatory modification on other proteins, which has spurred the development of methods to profile lysine methylation sites more globally. As with many posttranslational modifications, tandem mass spectrometry represents an ideal platform for the high-throughput analysis of lysine methylation due to its high sensitivity and resolving power. The following protocol outlines a general method to assay lysine methylation across the proteome using SILAC and quantitative proteomics. First, cells are labeled by SILAC to allow for relative quantitation across different experimental conditions, such as cells with or without ectopic expression of a methyltransferase. Next, cells are lysed and proteins are digested into peptides. Methylated peptides are then enriched by immunoprecipitation with pan-specific antibodies against methylated lysine. Finally, the enriched peptides are analyzed by LC-MS/MS to identify methylated peptides and their modification sites and to compare the relative abundance of methylation events between different conditions. This approach should yield detection of a couple hundred lysine methylation sites, and those showing differential abundance may then be prioritized for further study.

Original languageEnglish
Title of host publicationPost-translational Modifications That Modulate Enzyme Activity
EditorsBenjamin A. Garcia
PublisherAcademic Press Inc.
Number of pages24
ISBN (Print)9780128186695
StatePublished - 2019

Publication series

NameMethods in Enzymology
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988


  • Affinity purification
  • Lysine methylation
  • Mass spectrometry
  • Posttranslational modifications


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