DMTMM

[ShenXipeng]

Congratulations! you guys have done great works in the past and I hope you achieve greater success in the future.
Recommendation: a new crosslink reagent calld DMTMM developed by Ruedi Aebersold 2014 PNAS. was now gradually used by researchers. You can consider adding it to your program.

[01joy]

Hi ShenXipeng,

Thanks for using pLink.

Here is the tutorial for adding a new linker in pLink2:

1. Click Options→Meta Data Configuration
2. Select Linkers tab
   
3. Click Add, fill in linker information in the dialog
   
4. Click Update and then Save
5. Close pConfig window, the new linker will appear in Linkers ListView
   

Linker information needed:

• Name: the name of the new linker. Please make sure the linker name contains only alphanumeric characters and underlines. DO NOT add any special characters into the linker name, such as the whitespaces and ampersands (&).
• AlphaSites: the first cross-linked amino acid, parentheses “(” and “)” denote the peptide N terminus and C terminus, respectively; square brackets “[“ and “]” denote the protein N terminus and C terminus, respectively.
• BetaSites: the second cross-linked amino acid, “(”, “)”, “[“, and “]” denote the same as AlphaSites.
• LinkerMass: monoisotopic linker mass in inter/loop links.
• MonoMass: monoisotopic linker mass in mono links.
• LinkerComposition: linker composition in inter/loop links.
• MonoComposition: linker composition in mono links.
• LongMass: the longer mass in cleavable linker, 0 for uncleavable linker.
• ShortMass: the shorter mass in cleavable linker, 0 for uncleavable linker.

For parameter format, you can take BS3 as an example.

-------------
Best regards,
The pLink Team of pFind Lab
Institute of Computing Technology
Chinese Academy of Sciences
plink@ict.ac.cn
http://pfind.ict.ac.cn

[ShenXipeng]

That's really help! Thanks a lot.