Nano-liquid chromatography and capillary electrochromatography hyphenated with mass spectrometry for tryptic digest protein analysis: a comparison.

Nano-LC and CEC were studied for the separation of cytochrome c tryptic digest. The peptides mixture was analyzed using either a nano-LC commercial or a laboratory assembled instrumentation coupled with an IT-ESI-MS by using a nanospray interface. CEC experiments were carried out with a CE apparatus coupled with the IT-ESI-MS through a liquid junction interface. Analytes were separated utilizing C18 silica based stationary phases, of different properties and origin, silica derivatized with cyano groups and C18 monolithic material. The last column, just because the chemical composition (absence of charged/chargeable groups) was tested only using nano-LC. Best results mainly related to the highest number of peptides separated and column equilibration time were obtained by nano-LC employing the C18 stationary phase (detection of 20 peptides, coverage of 88%). Similar results were achieved using both commercial and laboratory assembled instrumentation. The use of CEC revealed a higher separation efficiency and shorter analysis time. However, the number of separated peptides were lower than those observed in nano-LC. In CEC the use of capillaries packed with cyanosilica particles offered better results; however, less satisfactory than those observed in the miniaturized LC technique. Provided the use of the same stationary phase and taking into account the driving forces, the two techniques can be considered complementary, offering different information related to the retention times of the studied peptides.