tims TOF to mzML conversion

Vladimir Gorshkov

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Mar 29, 2019, 1:14:40 PM3/29/19

to ProteomicsQA

Hello everybody,

does anybody have experience with converting timsTOF Pro datafiles to some open formats? How good/bad is support for this in, for example, ProteoWizard? The proteowizard site says that they only support BAF files (i.e. without mobility dimension), however there is also some threads in the forum that claim TDF 3.0 is supported. It is especially interesting to know how the IMS dimension is handeled. Any information is welcome.

Best regards,

Vladimir

Brian Pratt

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Mar 29, 2019, 2:08:56 PM3/29/19

to Vladimir Gorshkov, ProteomicsQA

Hi Vladimir,

Fully supported in msconvert. Can you point me at the page on the ProteoWizard site that indicated otherwise? That's clearly stale and needs fixing, though I can't seem to find it.

I'd say just download msconvert and start playing with it to see what you think. You'll find that the output files are quite large, but then so are the input files.

Cheers

Brian Pratt

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Vladimir Gorshkov

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Mar 29, 2019, 3:52:00 PM3/29/19

to ProteomicsQA

Hi Brian,

thank you for your answer. I will "play" with it then.

I loooked on the page with supported formats http://proteowizard.sourceforge.net/formats/index.html

Best regards,

Vladimir

On Friday, March 29, 2019 at 7:08:56 PM UTC+1, Brian Pratt wrote:

Hi Vladimir,

Fully supported in msconvert. Can you point me at the page on the ProteoWizard site that indicated otherwise? That's clearly stale and needs fixing, though I can't seem to find it.

I'd say just download msconvert and start playing with it to see what you think. You'll find that the output files are quite large, but then so are the input files.

Cheers

Brian Pratt

On Fri, Mar 29, 2019 at 10:14 AM Vladimir Gorshkov <hom...@gmail.com> wrote:

Hello everybody,

does anybody have experience with converting timsTOF Pro datafiles to some open formats? How good/bad is support for this in, for example, ProteoWizard? The proteowizard site says that they only support BAF files (i.e. without mobility dimension), however there is also some threads in the forum that claim TDF 3.0 is supported. It is especially interesting to know how the IMS dimension is handeled. Any information is welcome.

Best regards,
Vladimir

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