Comparison of microscale cleaning procedures for (Glyco) proteins prior to positive ion matrix-assisted laser desorption ionization mass spectrometry

Microscale cleaning procedures for peptides, proteins and glycoproteins prior to matrix-assisted laser desorption ionization (MALDI) mass spectrometric (MS) analysis, based on different mechanisms - drop dialysis, ultrafiltration, reverse phase adsorption and gelfiltration, are being compared. The selected standard (glyco) proteins cover the mass range of 5000-70 000 Da. Individual components and mixtures containing up to five components have been used for the investigation. Five different procedures were applied and evaluated with regard to a subsequent positive ion MALDI time-of-flight MS analysis, which requires samples with relative low salt/buffer content. All methods were adapted for protein samples in the low picomole range. Drop dialysis, ultrafiltration, reverse phase adsorption in two different forms and gelfiltration are shown to be useful for proteins and partially for peptides and glycoproteins. It turned out that glycoproteins are more difficult to handle, due to the relatively high sample losses during the desalting procedures. Gelfiltration and reverse phase adsorption are the least time consuming methods, whereas drop dialysis and ultrafiltration are well suited for working on many samples in parallel. However, reverse phase adsorption and ultrafiltration offer the highest enrichment factors. For proteins available only in large sample volumes gelfiltration and reverse phase adsorption are the methods of choice. (C) 1998 Elsevier Science B.V. All rights reserved.