Analysis of ubiquitinated proteome by quantitative mass spectrometry

Chan-Hyun Na, Junmin Peng

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Protein modification by ubiquitin (Ub) is one of the most common posttranslational events in eukaryotic cells. Ubiquitinated proteins are destined to various fates such as proteasomal degradation, protein trafficking, DNA repair, and immune response. In the last decade, vast improvements of mass spectrometry make it feasible to analyze the minute amount of ubiquitinated components in vivo. When combined with quantitative strategies, such as stable isotope labeling with amino acids in cell culture (SILAC), it is capable of profiling ubiquitinated proteome under different experimental conditions. Here, we describe a procedure to perform such a study, including differential protein labeling by the SILAC method, enrichment of ubiquitinated species, mass spectrometric analysis, and quality control to reduce false positives. The potential challenges and limitations of the procedure are also discussed.

Original languageEnglish (US)
Title of host publicationQuantitative Methods in Proteomics
Pages417-429
Number of pages13
Volume893
DOIs
StatePublished - 2012
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume893
ISSN (Print)10643745

Fingerprint

Proteome
Mass Spectrometry
Ubiquitinated Proteins
Isotope Labeling
Eukaryotic Cells
Protein Transport
Ubiquitin
DNA Repair
Quality Control
Proteins
Cell Culture Techniques
Amino Acids

Keywords

  • Mass spectrometry
  • Proteomics
  • SILAC
  • Ubiquitin

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Na, C-H., & Peng, J. (2012). Analysis of ubiquitinated proteome by quantitative mass spectrometry. In Quantitative Methods in Proteomics (Vol. 893, pp. 417-429). (Methods in Molecular Biology; Vol. 893). https://doi.org/10.1007/978-1-61779-885-6_26

Analysis of ubiquitinated proteome by quantitative mass spectrometry. / Na, Chan-Hyun; Peng, Junmin.

Quantitative Methods in Proteomics. Vol. 893 2012. p. 417-429 (Methods in Molecular Biology; Vol. 893).

Research output: Chapter in Book/Report/Conference proceedingChapter

Na, C-H & Peng, J 2012, Analysis of ubiquitinated proteome by quantitative mass spectrometry. in Quantitative Methods in Proteomics. vol. 893, Methods in Molecular Biology, vol. 893, pp. 417-429. https://doi.org/10.1007/978-1-61779-885-6_26
Na C-H, Peng J. Analysis of ubiquitinated proteome by quantitative mass spectrometry. In Quantitative Methods in Proteomics. Vol. 893. 2012. p. 417-429. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-885-6_26
Na, Chan-Hyun ; Peng, Junmin. / Analysis of ubiquitinated proteome by quantitative mass spectrometry. Quantitative Methods in Proteomics. Vol. 893 2012. pp. 417-429 (Methods in Molecular Biology).
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