Intensity in TopPIC or TopDIFF

[Mozhgan Boroumand]

Dear all,

I have a basic question; how does TopPIC (or TopDIFF) calculate the protein abundance? I mean what algorithm does it use for this calculation? 

I tried to compare it with the peak detection algorithm in FreeStyle but they are so different.  

Thank you in advance,

Mozhgan

[Liu, Xiaowen (Kevin)]

Hi, Mozhgan,

 

TopPIC uses proteoform feature intensities reported by TopFD as protein abundances. To compute proteoform feature intensities, TopFD sums up the intensities of all isotopic peaks of a proteoform across different charge states and MS1 scans as its intensity.

 

Please let me know if you have any other questions.

 

Best,

 

Xiaowen (Kevin)

 

From: top-dow...@googlegroups.com <top-dow...@googlegroups.com> on behalf of Mozhgan Boroumand <mojgan.b...@gmail.com>
Date: Wednesday, January 31, 2024 at 8:07 AM
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Subject: [ms-align-plus-pipeline] Intensity in TopPIC or TopDIFF

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[Mozhgan Boroumand]

Thank you so much for replying. But why when I try to do it manually (sums the intensities of isotopic peaks), the final value is much lower vs the TopPIC report? 

Thanks again,

Mozhgan

[Liu, Xiaowen (Kevin)]

Hi, Mozhan,

 

You need to sum up the intensities of isotopic peaks (XIC) in all MS1 scans and multiple charge states.

 

Xiaowen

 

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