What Are the Current Limitations of the SWATH® Variable Window Calculator Tool?

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

Answer

The SWATH® Variable Window Calculator tool enables users to build an optimized variable window SWATH data-independent acquisition (DIA) method specifically for a proteome of interest. The tool consists of a spreadsheet that calculates and scales the window size across the m/z range depending on the number of precursors found in that m/z range. That is, the Q1 window widths are varied over the m/z range so that each window contains a constant density from an intensity-weighted histogram of the survey scan data versus m/z.

The current limits for specific instruments are listed below:

Maximum target number of Q1 windows:

• 100 windows for TripleTOF® 5600+ system
• 200 windows for TripleTOF 6600 system
• 200 windows for the X500 series system
• 200 windows for the ZenoTOF 7600 system

• 1250 m/z for TripleTOF 5600+ system
• 2250 m/z for TripleTOF 6600 system
• 2250 m/z for the X500 series system
• 2250 m/z for ZenoTOF 7600 system