Dear Natalie,

Thank You for your detailed answer. I will look into msconvert.

Im actually not sure about this part:

> [Advanced option, default OFF] --precursorFromFilterLine: only
>      try to get the precursor MZ value from the Thermo
>      "filterline" text; only use this if you have a good reason!
>      Otherwise, the program first will try to obtain a more accurate
>       mass from the "Monoisotopic M/Z:" "trailer value"
>

There is a command line option? But I have not seen it the help menu   
of readw. (readw.exe -h)!
In our case the syntax would be "readw.exe -- 
precursorFromFilterline"; is that correct?

How can I see the other advanced options?

Thank you very much.
best
Dominik

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