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pFindStudio / pLink2

pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
http://pfind.ict.ac.cn/software/pLink/index.html
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MS cleavable cross-linking #29

Closed KamalMandal closed 6 years ago

KamalMandal commented 6 years ago

Does pLink2 support MS-Cleavable cross linker? Is Leiker_clv MS-cleavable (listed in the cross linker list of plink2)?

01joy commented 6 years ago

Hi @KamalMandal ,

pLink2 supports DSSO, the MS-cleavable cross-linker used in Liu F, Rijkers D T S, Post H, et al. Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry[J]. Nature methods, 2015, 12(12): 1179.

For more about DSSO supported in pLink2, please see #22 and #24 .

The Leiker_clv is not an MS-cleavable cross-linker. It is a trifunctional cross-linker. It is a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation.

The clv in Leiker_clv means the biotin can be cleaved out. For more details about Leiker, please see Tan D, Li Q, Zhang M J, et al. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states[J]. Elife, 2016, 5.

KamalMandal commented 6 years ago

Thanks a lot @01joy for your help. Is there any plan to introduce MS cleavable feature in Leiker_clv in near future? I think that would decrease the computational complexity drastically? Is there any commercial organization from where Leiker_clv can be procured?

01joy commented 6 years ago

Hi @KamalMandal ,

Sorry for the late reply, I am a programmer, and not quite familiar with the wet experiment and the cross-linker development.

The MS-cleavable can really decrease the computational complexity, but it requires MS3 and special data acquisition, which seems a little bit complicated. While with pLink2, you can also analyze non-cleavable data very efficiently.

As my collaborator who developed the Leiker is out for ASMS these days, I will give you a more detailed reply after she comes back.

Thanks for using Leiker and pLink2.

armadillocommander commented 6 years ago

@01joy

I talked with them yesterday, I’ll try to ask them if I meet with them tomorrow.

01joy commented 6 years ago

Hi @armadillocommander ,

Thank you for your contributions to this community.

01joy commented 6 years ago

Hi all,

You can purchase Leiker cross-linker from here: http://www.jkchemical.com/en/products/A012138035.html. Thanks for your support to pLink and Leiker.