Liquid Chromatography Electron Capture Dissociation Tandem Mass Spectrometry (LC-ECD-MS/MS) Versus Liquid Chromatography Collision-Induced Dissociation Tandem Mass Spectrometry (LC-CID-MS/MS) for the Identification of Proteins

J Am Soc Mass Spectrom. 2007 May;18(5):891-7. doi: 10.1016/j.jasms.2007.01.008. Epub 2007 Mar 9.


Electron capture dissociation (ECD) offers many advantages over the more traditional fragmentation techniques for the analysis of peptides and proteins, although the question remains: How suitable is ECD for incorporation within proteomic strategies for the identification of proteins? Here, we compare LC-ECD-MS/MS and LC-CID-MS/MS as techniques for the identification of proteins. Experiments were performed on a hybrid linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer. Replicate analyses of a six-protein (bovine serum albumin, apo-transferrin, lysozyme, cytochrome c, alcohol dehydrogenase, and beta-galactosidase) tryptic digest were performed and the results analyzed on the basis of overall protein sequence coverage and sequence tag lengths within individual peptides. The results show that although protein coverage was lower for LC-ECD-MS/MS than for LC-CID-MS/MS, LC-ECD-MS/MS resulted in longer peptide sequence tags, providing greater confidence in protein assignment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cattle
  • Chromatography, High Pressure Liquid / methods*
  • Molecular Sequence Data
  • Peptide Mapping / methods*
  • Proteins / chemistry*
  • Proteomics / methods
  • Spectroscopy, Fourier Transform Infrared*
  • Tandem Mass Spectrometry*


  • Proteins