Hello, I'm developing a tool for assessing quality of DIA experiments. I am using data from PXD017703 as an example of diaPASEF. When I look at Supplementary Figure 1 of the associated paper (https://doi.org/10.1038/s41592-020-00998-0), it seems apparent that the authors are defining their isolation windows both by boundary m/z values and by boundary ion mobility values. When I look inside the mzMLs created by TIMSConvert from these raw data, however, I see isolationWindow sections that specify only isolation window target m/z, isolation window lower offset, and isolation window upper offset; there's no mention of ion mobility boundaries.
Could you advise me on how to find the ion mobility boundaries of diaPASEF experiment isolation windows?
Thanks for this very helpful project!
Hello, I'm developing a tool for assessing quality of DIA experiments. I am using data from PXD017703 as an example of diaPASEF. When I look at Supplementary Figure 1 of the associated paper (https://doi.org/10.1038/s41592-020-00998-0), it seems apparent that the authors are defining their isolation windows both by boundary m/z values and by boundary ion mobility values. When I look inside the mzMLs created by TIMSConvert from these raw data, however, I see isolationWindow sections that specify only isolation window target m/z, isolation window lower offset, and isolation window upper offset; there's no mention of ion mobility boundaries.
Could you advise me on how to find the ion mobility boundaries of diaPASEF experiment isolation windows?
Thanks for this very helpful project!