Adding a New Fragmentation Rule for EAD Data from a ZenoTOF 7600 System to the Mascot Server


日期: 09/14/2022
类别: Academia Omics , Mass Spectrometers

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


Answer

The steps for adding Mascot server fragmentation rules for an electron activated dissociation (EAD) cell on a ZenoTOF 7600 system are as follows:
1) The fragmentation rules first need to be defined in the Mascot server. To do this, use the latest version of the Mascot server software, version 2.6 or higher. The fragmentation rules for the Mascot server are under the menu path: All Programs -> Mascot server -> Configuration -> Instruments. 

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2) Once the Instrument button is selected (see above), you will be able to see default fragmentation rules: Mascot Server -> Configuration Editor -> Instruments editor.

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In this view above, you can change the fragmentation rules for the EAD cell by selecting a new instrument.

3) The general naming conventions for peptide fragments are described here: https://www.matrixscience.com/help/fragmentation_help.html. We recommend selecting the following fragment ion for a dataset acquired on a ZenoTOF system using EAD fragmentation (last column labeled EAD SCIEX).   User-added image

4) Mascot Daemon is a client application that can be used to automate data file submission to the Mascot server; the new fragmentation rule can be used with either version 2.6 or 2.8 of Mascot Daemon. The newly created SCIEX EAD fragmentation rule can be selected in Mascot Daemon under the Parameter Editor tab.Mascot Daemon EAD selection.JPG