Complex Mixture Analysis


Analysis of complex protein mixtures, such as cell extracts, uses the same principles of protein identification as simple mixture proteins, but with some differences.

  • longer chromatography runs
  • possible two dimensional separation of peptides
  • much longer data analysis

A longer chromatography gradient can give more separation of peptides. More important, it gives the mass spectrometer time to measure more peptides. In a gradient of 1% acetonitrile/minute, in the 6 seconds to change from 30% to 30.1% acetonitrile, the instrument can analyze 18 peptides. Using a gradient of 0.25% acetonitrile/min, 72 peptides can be analyzed, allowing more proteins to be found.

In some cases, the peptide mixture is fractionated by ion exchange or other method before the reverse phase separation mentioned above. This is 2D-LC, referred to as MUDPIT by some. This increases the number of analyses.