Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics

Commun Biol. 2021 Mar 1;4(1):265. doi: 10.1038/s42003-021-01797-9.

Abstract

Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for 'all-in-one' one-pot sample preparation. This 'all-in-one' method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Breast Neoplasms / metabolism*
  • Breast Neoplasms / pathology
  • Chromatography, Liquid
  • Female
  • Glucosides / chemistry*
  • Humans
  • Lung Neoplasms / metabolism*
  • Lung Neoplasms / secondary
  • MCF-7 Cells
  • Mice
  • Neoplasm Micrometastasis
  • Neoplasm Proteins / metabolism*
  • Neoplastic Cells, Circulating / metabolism*
  • Neoplastic Cells, Circulating / pathology
  • Proteome*
  • Proteomics*
  • Single-Cell Analysis*
  • Spectrometry, Mass, Electrospray Ionization
  • Surface-Active Agents / chemistry*
  • Tandem Mass Spectrometry

Substances

  • Glucosides
  • Neoplasm Proteins
  • Proteome
  • Surface-Active Agents
  • dodecyl maltoside