How to create a new reference file for IntelliStart to use - WKB49211

OBJECTIVE or GOAL

Create a new calibration reference file for use within IntelliStart.

ENVIRONMENT

• MassLynx
• SYNAPT G2-Si

PROCEDURE

1. With MassLynx closed, open C:\MassLynx\Ref and copy in or create a new reference file.
2. If creating a new reference file from scratch or using an existing reference file from a previous installation, ensure that the layout/syntax matches that of the current installation's example reference files (see Additional Information below).
3. Once the reference file has been saved, browse to the C:\MassLynx\Intellistart\Configuration\ReferenceFile.xml.
4. Make a copy of this XML file as a backup, and then right-click and open it with Notepad.
5. Insert the new entry between the lines <ReferenceFiles> and </ReferenceFiles> (see example below).
6. Ensure that the format matches the existing entries. (Note that the full path must be given and that it is case-sensitive.)
7. When edits are complete, save the file.
8. Exit Notepad.
9. Open MassLynx and verify that IntelliStart shows the new file.

ADDITIONAL INFORMATION

With respect to a reference file layout, here are some important notes. 

a - Any line that starts with a semicolon will not be read as a reference mass.

b - The line ;Parent=xxx.xxxx specifies the parent mass if the reference file is to be used in MSMS.

c - The line ;CE=xx specifies the collision energy that IntelliStart will use by default with the reference file. If fragmentation is required, this should be set to an appropriate value.

d - To the right of every reference file is a second value signifying the relative intensity (%) of each reference peak when compared with the reference peak that is most intense (labeled 100).