PD2.5 Phosphopeptide

[hyoungjoolee]

I am new to PD2.5+MSFragger for phosphopeptides. In one process workflow, I created two search engines (MSFragger and Sequest).

The goal was to determine how much overlap there was between the two engines in terms of phosphopeptides. The two do not overlap(for phosphopeptides). There seems to be a difference between the two engines in the way they display peptides, resulting in different peptides being considered.

[huiyinc]

Hi,

I checked my result and there are peptides with their modifications commonly identified by MSFragger and Sequest (as the attached file). I am not sure what happened with your analysis, but I can help with checking the data if you are fine to share it with me.

Best wishes,

Huiyin

hyoungjoolee @.***> 於 2023年4月1日 上午12:37 寫道：



I am new to PD2.5+MSFragger for phosphopeptides. In one process workflow, I created two search engines (MSFragger and Sequest).

The goal was to determine how much overlap there was between the two engines in terms of phosphopeptides. The two do not overlap(for phosphopeptides). There seems to be a difference between the two engines in the way they display peptides, resulting in different peptides being considered.

[image: PD25phospho] https://user-images.githubusercontent.com/46012174/229178879-f674f012-34e9-42c9-ada2-597b0c482a96.JPG

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[hyoungjoolee]

Hi Huiyin

Thank you.

1. I have searched for it again only using MSFragger. In the image, N-terminal acetylation and phosphorylation are shown as mass shifts, while carbamidomethyl is shown as normal.

2. Can you take a look a the PWF and CWF (I have attached them) MSFragger_PWF_CWF.zip

3. Is the MSFragger compatible with PD3.0? Your image shows PD version 3.0. Did you just open it with PD 3.0?

Thank you again for taking care of my issue

[huiyinc]

Hi,

Sorry for the late reply. It took me some time to update MSFragger-PD node. A pre-release has been uploaded to: https://github.com/Nesvilab/PD-Nodes/releases/tag/1.2.0 Can you please download and try it? It should resolve the issue.

For your last question: Yes, I open the result using PD v3.0, but the MSFragger-PD node is currently not compatible with PD v3.0. We are working on it, but can't be sure when it will be ready (hopefully soon).

Best,

Huiyin

hyoungjoolee @.***> 於 2023年4月4日 週二 上午1:06寫道：

Hi Huiyin

Thank you.

1.

I have searched for it again only using MSFragger. In the image, N-terminal acetylation and phosphorylation are shown as mass shifts, while carbamidomethyl is shown as normal. [image: MSFragger_PD2 5] https://user-images.githubusercontent.com/46012174/229576811-f2358a3d-c7e1-43e2-8d79-7e1c1ad94108.PNG 2.

Can you take a look a the PWF and CWF (I have attached them) MSFragger_PWF_CWF.zip https://github.com/Nesvilab/PD-Nodes/files/11140677/MSFragger_PWF_CWF.zip 3.

Is the MSFragger compatible with PD3.0? Your image shows PD version 3.0. Did you just open it with PD 3.0?

Thank you again for taking care of my issue

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[hyoungjoolee]

Hi Huiyin

Thank you for taking care of my issue. The new node has been installed and the search has been rerun. Yes, it works!

Thanks again!!