PASEF data complete submission

[wanghe98]

Dear PRIDE team,

We would like to upload our DDA-PASEF and diaPASEF raw data (Bruker .d format) to PRIDE to form a complete submission.

Now, we have the 1) .d raw data, 2) mzML converted from .d, 3) mzIdentML or mzTab converted from the database search results (The database search was directly conducted by FragPipe or DIA-NN based on .d raw files which is a highly recommended way).

However, when submission, the mzML files have lost ion mobility information and cannot be connected with the corresponding mzIdentML or mzTab. We would like to ask:

**1. If the database search was conducted directedly based on .d PASEF raw data, is it impossible currently to achieve a complete submission?

2. Is this because currently, the mzML format cannot support ion mobility very well?

3. To achieve a complete submission, if I have to convert .d to mzML first, then do database search using these mzML files (although this way is highly unrecommented by the common database search software)?**

Thanks very much!