Development and evaluation of a micro- and nanoscale proteomic sample preparation method

J Proteome Res. Nov-Dec 2005;4(6):2397-403. doi: 10.1021/pr050160f.


Challenges associated with the efficient and effective preparation of micro- and nanoscale (micro- and nanogram) clinical specimens for proteomic applications include the unmitigated sample losses that occur during the processing steps. Herein, we describe a simple "single-tube" preparation protocol appropriate for small proteomic samples using the organic cosolvent, trifluoroethanol (TFE) that circumvents the loss of sample by facilitating both protein extraction and protein denaturation without requiring a separate cleanup step. The performance of the TFE-based method was initially evaluated by comparisons to traditional detergent-based methods on relatively large scale sample processing using human breast cancer cells and mouse brain tissue. The results demonstrated that the TFE-based protocol provided comparable results to the traditional detergent-based protocols for larger, conventionally sized proteomic samples (>100 microg protein content), based on both sample recovery and numbers of peptide/protein identifications. The effectiveness of this protocol for micro- and nanoscale sample processing was then evaluated for the extraction of proteins/peptides and shown effective for small mouse brain tissue samples (approximately 30 microg total protein content) and also for samples of approximately 5000 MCF-7 human breast cancer cells (approximately 500 ng total protein content), where the detergent-based methods were ineffective due to losses during cleanup and transfer steps.

Publication types

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

MeSH terms

  • Animals
  • Brain / metabolism
  • Breast Neoplasms / metabolism
  • Cell Line, Tumor
  • Detergents / pharmacology
  • Humans
  • Male
  • Mass Spectrometry
  • Mice
  • Nanotechnology / methods*
  • Peptides / chemistry
  • Proteins / chemistry
  • Proteome
  • Proteomics / instrumentation*
  • Proteomics / methods*
  • Solvents
  • Time Factors
  • Trifluoroethanol / chemistry


  • Detergents
  • Peptides
  • Proteins
  • Proteome
  • Solvents
  • Trifluoroethanol