Improvement of performance in label-free quantitative proteome analysis with monolithic electrospray ionization emitter

Abstract

The postcolumn void volume, which is introduced by the connecting tubing and void ESI emitter in the nanoflow LC coupled with MS/MS system (μLC-MS/MS), is harmful for the analysis of peptides in shotgun proteome analysis. A new type of porous C12 monolithic ESI emitter was prepared to eliminate the disruption and mixing effects occurring in the connecting tubing and void emitter. It was demonstrated that the porous hydrophobic monolith inside the emitter played a key role in retaining the good peak profile, and the average peak capacity of the whole separation system increased 12.8% in contrast to commercially available void emitter. Then, the porous C12 monolithic emitter was applied in label-free quantitative proteome analysis of two standard protein mixtures that were spiked into the tryptic digest of mouse livers extract. Compared to commercially available void ESI emitter, the number of proteins with reliable results in quantification increased greatly. And the relative quantities of the four standard proteins were all determined with the relative error ≤6.8%. However, quantitative information of only three standard proteins could be obtained when void emitter was used. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.