Issue77

Title endogenous peptides setup
Priority question Status chatting
Superseder Nosy List kfwang, liuxiao
Assigned To Keywords

Created on 2022-04-20.16:48:08 by liuxiao, last changed by kfwang.

Files
File name Uploaded Type Edit Remove
1.png kfwang, 2022-04-22.10:11:03 image/png
Messages
msg225 (view) Author: kfwang Date: 2022-04-27.10:36:03
Dear, If non-specific cleavage is selected in pFind, the choice of enzyme species 
will only bring about a small difference in the results. Considering your needs, we 
recommend choosing noenzyme and setting up non-specific cleavage.
msg224 (view) Author: liuxiao Date: 2022-04-25.22:26:12
thank you, I notice that when I choosed different enzyme types such as trypsin 
and formic acid D_C in different non-specific searches with the other parameters 
unchanged, I got two different results finally. That means the enzyme type could 
affect the final result even in the non-specific type. 
When I search endogenous peptides in Mascot or Peaks, the "none" enzyme type is 
suggested in manual. 
Is there perferred enzyme type in pFind when I search endogenous peptides ?
msg223 (view) Author: kfwang Date: 2022-04-24.11:10:48
Dear, endogenous peptides are not usually produced by protein digestion, but are 
naturally present in the body I think. Therefore, they may not meet the rules of 
enzyme digestion and need to be searched by non-specific.
msg222 (view) Author: liuxiao Date: 2022-04-22.15:12:32
Thank you!
And there is a another question, when I choose the "Non-specific" parameter, is  
there any limitation of the enzyme type in endogeous peptides search? Or dose it 
mean that any enzyme I could choose will be OK?
msg221 (view) Author: kfwang Date: 2022-04-22.10:11:03
Dear, When searching for endogeous peptides, please select the Non-Specific 
parameter, or check the open search option. Both options are marked in the attached 
image.
msg217 (view) Author: liuxiao Date: 2022-04-20.16:48:08
hi, I have some questions about endogeous peptides search. 
When I search the endogenous peptides, how should I set the enzyme selection in 
pFind. 
And is there any other notice when I search the endogeous peptides by pFind?
History
Date User Action Args
2022-04-27 10:36:06kfwangsetmessages: + msg225
2022-04-25 22:26:15liuxiaosetmessages: + msg224
2022-04-24 11:10:52kfwangsetmessages: + msg223
2022-04-22 15:12:35liuxiaosetmessages: + msg222
2022-04-22 10:11:07kfwangsetfiles: + 1.png
messages: + msg221
2022-04-22 10:09:32kfwangsetmessages: - msg220
2022-04-22 10:09:20kfwangsetmessages: + msg220
nosy: + kfwang
2022-04-22 09:37:07kfwangsetstatus: unread -> chatting
2022-04-20 16:48:11liuxiaocreate