Converting Orbitrap Eclipse files to mzML

[Laura Muehlbauer]

I'm using TPP for the first time, so I apologize if this has been resolved elsewhere. I'm trying to convert some files from a Thermo Eclipse to mzML and I get an unknown instrument error and the conversion fails. Is there a way to bypass this?

[David Shteynberg]

Hi Laura,

Can you try downloading the latest version of msconvert and replacing your copy in C:/TPP/bin or where you currently have it installed?  Once you get an mzML file you can copy it to your TPP data directory and run the search, validation, etc.  Let us know how it goes.

Cheers,

-David

On Wed, Sep 30, 2020 at 12:10 PM Laura Muehlbauer <muehlba...@gmail.com> wrote:

I'm using TPP for the first time, so I apologize if this has been resolved elsewhere. I'm trying to convert some files from a Thermo Eclipse to mzML and I get an unknown instrument error and the conversion fails. Is there a way to bypass this?

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[Jason Winget]

It might also be worth trying the --ignoreUnknownInstrumentError flag in your mzML command.

We had a similar problem with a new Thermo instrument where it wasn't supported yet, and this flag just skips the check on the instrument ID.

[Laura Muehlbauer]

Both worked! Thanks so much!