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Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
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Precursor Mass Mode in PD node #35

Closed wangrui85 closed 7 months ago

wangrui85 commented 10 months ago

image image Hi, Dears, here is questions about parameters in MSfragger. I found that in FragPipe is "corrected" for open search of spectral Processing. How to set it in PD node? Another problem is PSM results from PD only displayed detal mass absolute difference in Dalton between the theroetical mass of the peptide and the expected peptide below 250 Da. How to get larger mass difference in searching.

huiyinc commented 10 months ago

Hi,

For the first question, I think "Recalculated" equals to "corrected". For the second question, you may change the precursor mass tolerance upper/lower via the parameter panel.

Best wishes,

Huiyin

wangrui85 @.***> 於 2023年8月11日 週五 下午6:07寫道：

[image: image] https://user-images.githubusercontent.com/87349846/259977455-8f302078-2bc8-401a-ab9b-8aba53f32bc6.png [image: image] https://user-images.githubusercontent.com/87349846/259978031-9a626e83-fc80-444a-947e-7940548fded9.png Hi, Dears, here is questions about parameters in MSfragger. I found that in FragPipe is "corrected" for open search of spectral Processing. How to set it in PD node? Another problem is PSM results from PD only displayed detal mass absolute difference in Dalton between the theroetical mass of the peptide and the expected peptide below 250 Da. How to get larger mass difference in searching.

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/35, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA7ZM2OABCSHWL526EDXUX743ANCNFSM6AAAAAA3MWJWKY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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

wangrui85 commented 10 months ago

Thanks. solved. from 阿里邮箱 iPhone------------------------------------------------------------------ @.> 日　期：2023年08月11日 18:40:03 @.> @.>; @.> 主　题：Re: [Nesvilab/PD-Nodes] Precursor Mass Mode in PD node (Issue #35)

Hi,

For the first question, I think "Recalculated" equals to "corrected". For the second question, you may change the precursor mass tolerance upper/lower via the parameter panel.

Best wishes,

Huiyin

wangrui85 @.***> 於 2023年8月11日 週五 下午6:07寫道：

[image: image] https://user-images.githubusercontent.com/87349846/259977455-8f302078-2bc8-401a-ab9b-8aba53f32bc6.png [image: image] https://user-images.githubusercontent.com/87349846/259978031-9a626e83-fc80-444a-947e-7940548fded9.png Hi, Dears, here is questions about parameters in MSfragger. I found that in FragPipe is "corrected" for open search of spectral Processing. How to set it in PD node? Another problem is PSM results from PD only displayed detal mass absolute difference in Dalton between the theroetical mass of the peptide and the expected peptide below 250 Da. How to get larger mass difference in searching.

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/35, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA7ZM2OABCSHWL526EDXUX743ANCNFSM6AAAAAA3MWJWKY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>