Setting up a single-injection CID/EAD data-dependent acquisition (DDA) method for the ZenoTOF 7600 system

For research use only. Not for use in diagnostic procedures.

Answer

The ZenoTOF 7600 system employs two modes of fragmentation: 1) collision-induced dissociation (CID) and 2) electron-activated dissociation (EAD). Acquisition methods can be built in SCEIX OS software that use both CID and EAD fragmentation; this hybrid approach can be applied in the same data-dependent acquisition (DDA) method and has been shown to produce deep sequence coverage of a protein digest on a ZenoTOF 7600 system. Combining both fragmentation types into one method delivers the power of CID fragmentation for singly charged peptides and the unique patterns, isomer differentiation, and PTM analysis of EAD fragmentation.

In SCIEX OS software versions 3.0 and later, two IDA methods can be created within the same acquisition method: one for EAD and one for CID fragmentation. To create a hybrid method, select the Advanced dropdown menu in the MS Method workspace and then select the Show advanced parameters option. Begin a new acquisition method by choosing the New dropdown menu and adding the source parameters. In the Experiment section, select IDA from the dropdown menu (see screenshot).  

The second IDA can be created by adding an IDA experiment using the Add Experiment option on the left side of the method page.

Select EAD fragmentation for the first IDA experiment and then select CID fragmentation for the second. If the fragmentation mode is grayed out, select "Show EAD parameters" from the Options menu. Since these two events occur within the same duty cycle, the user needs to adjust the parameters for each event (e.g., number of precursors, TOF MS, and MS/MS accumulation times). The parameters provided in the SCIEX tech notes MKT-28039-A or MKT-31336-A can serve as a good starting point for optimization, depending on the sample needs.

This screenshot below shows the combined total scan time and some source parameters:

Here is an example of IDA method 1 with EAD fragmentation and its parameters. 

Here is an example of IDA method 2 with CID fragmentation: