The goals of this application note were to:

1)  Demonstrate the advantage of using exclusion lists with retention times and retention time windows with multiple injections of the same sample to increase the total number of proteins identified and the protein coverage for a complex sample with a wide dynamic range.

2)  Provide a “step by step” procedure to customers who want to implement this strategy with the help of Proteome Discoverer.

What does the application note illustrate?

Excluding previously identified peptides for subsequent LC-MS/MS analyses allows the characterization of more proteins and increases protein coverage of many of those proteins. This strategy can be implemented readily by customers who have an LTQ Orbitrap with our existing software solution: Proteome Discoverer and Xcalibur. We take advantage of the high mass accuracy of the Orbitrap to specifically exclude peptides  within a small mass tolerance window and a narrow retention time window.

To read/download the complete application note, please use the link on this page.