Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics

Takeshi Masuda, Naoyuki Sugiyama, Masaru Tomita, Sumio Ohtsuki, Yasushi Ishihama

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


We found that nuclear envelopes stabilize against surfactants in the presence of ethylene glycol (EG). We, therefore, developed a novel subcellular fractionation approach for proteomics using RIPA buffer containing EG and phase transfer surfactants. This method involves separating the cells into the cytoplasm, organelles, and nucleus, including intermediate filaments without ultracentrifugation. These fractions are directly applicable to sample preparation for shotgun proteomics as they have no mass spectrometry (MS)-incompatible chemicals, whereas those separated by traditional fractionation protocols require desalting. This protocol is successfully applied to subcellular fractionation with only 3.5 × 105 cells. Here, it was combined with phosphoproteomics and proteomics to identify phosphorylation sites regulating protein subcellular localization. In total, 59 phosphorylation sites on 42 phosphopeptides and 32 proteins showing different enrichment patterns between phosphoproteomics and the corresponding proteomics were identified, which are potential candidate sites to regulate the protein subcellular localization, including serine 706 on CD44 and serine 22 on lamin A/C.

Original languageEnglish
Pages (from-to)75-84
Number of pages10
JournalJournal of Proteome Research
Issue number1
Publication statusPublished - 2020 Jan 3


  • ethylene glycol
  • mass spectrometry-compatible method
  • phase transfer surfactant
  • phosphoproteomics
  • subcellular fractionation

ASJC Scopus subject areas

  • Biochemistry
  • General Chemistry


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