Fast and Effective Complex Sample Desalting for LC/MS/MS Analysis Using the Thermo Scientific Aspire RP30 Desalting Tips

April 2009

Mass spectrometry has become a powerful tool for the analysis of complex protein samples. Shotgun or bottom-up proteomics requires the analysis of thousands of peptides generated by an enzymatic digestion which can be achieved by using LC/MS/MS methods.

Highly complex samples often contain salts, detergents and other ion-suppressing contaminants that limit the ionization process resulting in lower peak intensities and compromised peptide/protein detection. It is therefore essential to remove this interference from the samples before subjecting them to MS analysis.

Here we report a fast and effective way to facilitate MS sample cleanup. Two desalting methods, the Thermo Scientific Aspire RP30 Desalting Tips and the traditional column flushing procedure, were employed to desalt a tryptic-digested yeast whole cell lysate (soluble fraction) prior to LC/MS/MS runs.

By performing this side-by-side comparison, we observed an 11% increase in total identified proteins, 26% increase in total identified peptides and 50% increase in total numbers of spectra with the sample desalted by the Aspire™ tips. Due to the reduction in ion-suppression effects, sequence coverage was also improved with the sample subjected to the Aspire tip cleanup.

In addition, the proprietary Styrene-divinylbenzene resin contained within the Aspire tips allows higher peptide recovery, which is better suited for desalting of complex samples. Overall, the 15-minute Aspire desalting protocol is fast and effective compared to the traditional 1 to 4-hour column flushing method.

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