To continue to improve the quality of the SWATH acquisition data that one can achieve in complex matrices, we are working on ways that we can decrease the size of the Q1 window, while still maintaining full mass range coverage and optimal cycle times.  One great way to do this is to use the variable window SWATH acquisition feature that will be available in Analyst TF software or SCIEX OS software. To achieve better specificity in complex matrices, smaller Q1 windows (red line) are used in the m/z dense regions where many peptide precursors are measured, wider windows are used where there are less precursors such that the entire mass range is still interrogated. The m/z density histograms (blue line) constructed from the TOF MS data for the proteome of interest (blue line) can be used to construct variable sized windows, where the density of precursors in each of the isolation windows is equalized across the m/z range (link to tool below).

• Improved data quality using variable Q1 window widths in SWATH acquisition, SCIEX technical note RUO-MKT-02-2879-B.
• Evolution of SWATH acquisition provides large gains in quantified proteins, SCIEX Technical note RUO-MKT-02-5772-A.
• SWATH acquisition improves metabolite coverage over traditional data dependent techniques for untargeted metabolomics. SCIEX technical note RUO-MKT-02-7128-A.
• Download the Variable Window Calculator

RUO-MKT-18-13709-A