Rapid protein identification using direct infusion nanoelectrospray ionization mass spectrometry

Proteomics. 2006 Jan;6(1):16-25. doi: 10.1002/pmic.200500043.


Current protein identification techniques are largely based on MALDI-TOF mass fingerprinting and LC-ESI MS/MS sequence tag analysis. Here we describe an improved method for rapid protein identification that uses direct infusion nanoelectrospray quadrupole time-of-flight (nanoESI QTOF) MS. Protein digests were analyzed without LC separation using nanoESI on a QSTAR XL MS/MS system in information dependent data acquisition mode. The protein identification conditions and parameters were extensively evaluated with in-solution and in-gel digested protein samples. Rapid identification of proteins was achieved and compared directly to the results obtained on the same samples using nanoflow HPLC-MS/MS on the QSTAR system. The increased throughput, reproducibility, the high data quality, and the ease of use make the direct infusion system an efficient and affordable technique for protein identification analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, High Pressure Liquid
  • Electrophoresis, Gel, Two-Dimensional
  • Nanotechnology
  • Proteins / chemistry*
  • Sensitivity and Specificity
  • Spectrometry, Mass, Electrospray Ionization / methods*


  • Proteins