TopFD Precursor assignment issue

[wingk...@gmail.com]

Hi,

This is Preston from CUHK.

I notice that in numerous deconvoluted MS2 spectra processed by TopFD, the assigned precursor ion m/z is inconsistent with that reported by the raw file and the mzml input file.

As a result, the precursor mass assigned to these spectra might be incorrect. In fact, for these spectra, the precursor mass are inconsistent with the precursor mass reported by other algorithms (e.g. Xtract and Thrash). For other spectra with precursor m/z correct assigned, their precursor mass are consistent with the mentioned algorithms. Is it possible that my parameters need to be tweaked a bit to ensure correct m/z assignment?

Examples and parameters described in this ppt

MzML

Deconvoluted files

Thanks!

Preston

[In Kwon Choi]

Hi Preston,

Thank you for the issue report. We will take a look into the issue and keep you updated.

Best,

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Have a nice day:)

In Kwon       Choi

[liuxia...@gmail.com]

Hi, Preston, 

The problem is that the precursor isolation window in the data file is 0.8 m/z, which is smaller than the default setting 3 m/z of TopPIC. You can test TopPIC on the data set by setting the precursor window to 0.8 m/z.

Best, 

Xiaowen

On Wednesday, September 29, 2021 at 9:14:58 AM UTC-5 liuxia...@gmail.com wrote:

Hi, Preston, 

Thank you for letting us know. We will look into it and keep you updated. 

Best, 

Xiaowen

[Lui Kin Wing]

Dear Dr. Liu,

Thank you for your reply.

In the data I share, the TopFD precursor window was already set to 0.8 m/z. Perhaps I should try 0.4 (therefore precursor +/- 0.4)?

The reason I use such small isolation window was because I was analysing histones. 3 m/z windows would result in multiple proteoform (e.g +/- methylations) co-isolated for MS2.

Yours sincerely,

Preston

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Sent: Wednesday, September 29, 2021 11:15:09 PM
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Subject: [ms-align-plus-pipeline] Re: TopFD Precursor assignment issue

 

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[liuxia...@gmail.com]

Hi, Preston, 

Setting the precursor window to 0.8 m/z was correct. You do not need to try 0.4. 

We will look into the data and keep you updated. 

Best,

Xiaowen