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.
On Wednesday, September 30, 2020 at 3:15:29 PM UTC-4 David Shteynberg wrote: > 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 <[email protected]> > 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? >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/2b97785c-9de6-4fd1-8bef-0f881c4e8f90n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/2b97785c-9de6-4fd1-8bef-0f881c4e8f90n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/3ad831c0-e2b1-42fa-9848-42c6c12e046bn%40googlegroups.com.
