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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Dimethylation quantification #1667

Open 2kleio opened 5 years ago

2kleio commented 5 years ago

Hi there, Now with the SILAC quantification, is it possible to allow quantification based on other MS1 labeling methods such as dimethylation (on N-term and Lys)? Thanks

trishorts commented 5 years ago

It is something that we can consider. Can you tell me a bit more about the level of multiplexing? Are the dimethyl reagents described in a publication or commercially available? We can guess at what you need but it's better to have more details.

rmillikin commented 5 years ago

https://www.ncbi.nlm.nih.gov/pubmed/25045933 I'm assuming?

There might be a way to hack together something with the current implementation but @zrolfs will need to chime in I think. He wrote the SILAC stuff.

zrolfs commented 5 years ago

Hi 2kleio, It is high on my priority list to implement and validate quantification for modification-based labeling, including TMT/iTRAQ, but the functionality does not currently exist.

As @rmillikin mentioned, a solution could be hacked together in the current release, but it would be dependent on the lysine being labeled to discriminate between conditions.

  1. Add your dimethyl tags to the modification list . Here's a mock example that may need to be tailored to your labels: ID DimethylationLightNTerm TG X PP Peptide N-terminal. MT Common Variable CF H4 C2 // ID DimethylationHeavyNTerm TG X PP Peptide N-terminal. MT Common Variable CF H{2}6 C2 H-2 //

  2. Specify these N-terminal modifications as variable modifications in your search task. This is imperfect, because it will allow for "mixtures" of light/heavy labels, as well as unlabeled peptide N-termini. A more elegant solution is forthcoming.

  3. Light/Unlabeled dimethylation of lysine already exists under the "Common Biological" modification list. Specify this label as a fixed modification.

  4. Use the SILAC labels to specify the isotope differences of the heavy label as though the heavy isotopes were on lysine instead of the dimethyl label.

  5. Search your data!

Let me know if you have any questions or run into any issues. Zach

acesnik commented 5 years ago

Likewise, I wonder if we have any use cases for NeuCode SILAC

2kleio commented 5 years ago

Thanks a lot for the quick reply. I will test it in the next couple of days and let you know.