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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
201 stars 38 forks source link

Supports for cross-linking searching? #79

Closed yanze039 closed 11 months ago

yanze039 commented 11 months ago

Hi Michael,

Thanks for this excellent project!

I have a specific problem and would like to know whether I can achieve it by modifying sage here.

I have a protein where many residues are randomly labeled by a known peptide. The linker is known. I have the LC-MS/MS data of this molecule (Trypsin degist). Now I want to find which residues of the protein are labeled by the peptide, i.e. to find the label positions.

So in general, it's more like a cross-linking searching task, but currently I haven't got an idea how to do it in sage.

Since Sage is the only project I can find which is totally open-source and friendly for coders, do you have idea when to support the crosslinking searching or can you give me some hints if I modify sage to my projects by myself?

Thanks in advance!

lazear commented 11 months ago

Hi Yanze

Unfortunately, I'm not very familiar with crosslinking searches or software. Kojak is an open-source project for performing XL searches - maybe worth giving it a shot?

I think it should be possible to do this in Sage - Based on this paper, it seems somewhat analogous to a open-search/mass-offset search + localization, with diagnostic ions from the known peptide (but again, I am not familiar with algorithms for searching XL data). This might not give you results as high quality as using a tool specifically designed for XL though.