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michalsta / opentims

Open-source C++ and Python module for opening binary timsTOF data files.
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timsTOF fleX supported? #3

Closed fangfeiz closed 3 years ago

fangfeiz commented 3 years ago

We would like to approach a set of timsTOF FleX diaPASEF data from scratch. We are wondering if opentims works on the timsTOF fleX data, such that theopentims_bruker_bridge libraries can be also applied to TimsTOF FleX data? A Flex's .d folder contains an analysis.tsf_bin as the data file, but not an analysis.tdf as usual in Pro data. We got this error:no such table: Frames if read a FleX's .d (We tested timsTOF Pro data using timsr and it worked)

MatteoLacki commented 3 years ago

Hi,

It depends on how Bruker designed the analysis.tsf_bin. I will ask them Friday during our biweekly meeting with them.

Cheers!

Mateusz Krzysztof Łącki

German tel. +49 159 01681376 Polish tel. +48 579 647 311 Skype: mathewin GitHub: MatteoLacki https://github.com/MatteoLacki

On Wed, Apr 28, 2021 at 6:36 PM FangfeiZ @.***> wrote:

We would like to approach a set of timsTOF FleX diaPASEF data from scratch. We are wondering if opentims works on the timsTOF fleX data, such that theopentims_bruker_bridge libraries can be also applied to TimsTOF FleX data? A Flex's .d folder contains an analysis.tsf_bin as the data file, but not an analysis.tdf as usual in Pro data. We got this error:no such table: Frames if read a FleX's .d (We tested timsTOF Pro data using timsr and it worked)

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MatteoLacki commented 3 years ago

Hi,

This is a different format and it was not meant to be supported by timspy/opentims which is meant to deal with timstof pro devices only. We might consider at some point asking Bruker for letting us know how to deal with this format, but this is not coming within the next few months for sure, sorry. You should check, however, if they do not offer an SDK on their website.

Best wishes,

On Wed 28. Apr 2021 at 18:36, FangfeiZ @.***> wrote:

We would like to approach a set of timsTOF FleX diaPASEF data from scratch. We are wondering if opentims works on the timsTOF fleX data, such that theopentims_bruker_bridge libraries can be also applied to TimsTOF FleX data? A Flex's .d folder contains an analysis.tsf_bin as the data file, but not an analysis.tdf as usual in Pro data. We got this error:no such table: Frames if read a FleX's .d (We tested timsTOF Pro data using timsr and it worked)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/michalsta/opentims/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6H2AHPEJF2CDNHPYSI5PDTLA2SBANCNFSM43XN3RHA .

fangfeiz commented 3 years ago

OK. Thanks for the inquiry. We will try for other solutions.