TMT on timstof

[rudnickp]

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• Describe the issue or question: When will we be able to process PASEF data for TMT reporter ions?

[fcyu]

It is one of the feature we are going to add in the near future. If everything goes well, it should be ready by the end of this year. Stay tuned.

Best,

Fengchao

[rudnickp]

Hi Fengchao, Can you elaborate on what the current incompatibilities are?

Thanks Paul

[fcyu]

Hi Paul,

FragPipe currently replies on Philosopher to 1) extract TMT channel intensities from MS2; and 2) extract MS1 intensity. However, Philosopher cannot read .d format or perform 4-D feature detection. Converting .d to .mzML does not solve the problem, as it still requires 4-D feature detection. Moreover, the conversion process is very time-consuming and requires a lot of disk space, which makes the user experience poor.

The solution is straightforward. Since FragPipe already has IonQuant that can perform 4-D feature, we just need to switch the aforementioned steps to use IonQuant. This feature request has been one of our top priorities. Should be available in the near future.

Best,

Fengchao

[rudnickp]

Thanks for your response. All makes sense. FYI- I have some very recent files from Bruker where the de-noising steps are done in real time, resulting in file sizes 10-100X smaller than previously. Perhaps this will help your effort.

Best Paul

[fcyu]

Hi Paul,

Thanks for the info. It will largely reduce the CPU time and memory requirements of the 4-D feature detection.

It would be great if you could share some of the testing data with us. I will send a link to upload the files if you need.

Best,

Fengchao

[rudnickp]

Yes, feel free to send a link.

[fcyu]

Sounds great! Here is the link: https://www.dropbox.com/request/VPQzvEtK8aU4t9CjwfDp

Thanks,

Fengchao

[witszymanski]

Hi all!

Any update in this field? Would be great to finally get rid of MQ.

Greets!

Witek

[GolAGitHub]

Hello there,

FragPipe v22.0 now has the option to use IonQuant as the instensity extraction tool. However, this appears to still be incompatible with Bruker .d files. Is this a bug or is this feature still under development?

Thank you.

[fcyu]

The support for the timsTOF TMT is still under development.

Best,

Fengchao

[camdouglas]

Hello,

I was wondering if anyone was able to get this feature to work. I usually work with DIA PASEF data from the Tims TOF Pro2 or with .RAW DDA files from an Orbitrap Fusion. Recently, I ran a TMT-10plex phosphoproteomic experiment with 6-fractions on the TimsTOF in DDA mode. I am currently struggling to identify the best way to analyze this and am interested in doing it with Fragpipe, however, I do not believe that I am configuring the software correctly. Does anyone have any guidance as to how I should proceed with this analysis in Fragpipe? Thanks.

Best, Cam

[fcyu]

We have a pre-released version that supports it. Contact yufeATumich.edu (replace AT with @) if you want to test the new version.

Best,

Fengchao