search

smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 46 forks source link

requesting a new enzyme #2041

Closed fazeliniah closed 3 years ago

fazeliniah commented 3 years ago

Dear MetaMorpheus developers. We are using a new enzyme for our bottom-up proteomics: https://www.sciencedirect.com/science/article/pii/S1535947620600172 ProAlanase cuts at the c-terminus of Ala and Pro. How is the best way to add a new enzyme to the database in MetaMorpheus? Thanks

mjfitzhenry commented 3 years ago

Yes, I would also like this enzyme added as an option in MM please

acesnik commented 3 years ago

Hi there,

Adding a new protease isn't a feature in MetaMorpheus, yet, but you can try adding a new protease manually by going to the ProteolyticDigestion\proteases.tsv file and adding a row for a new protease:

image image

It's not an ideal method, since there is no error checking for the additional entries (MetaMorpheus won't open if something is wrong), but it's something you could try.

acesnik commented 3 years ago

You can probably just copy-paste the Glu-C (with asp) line and change the name to ProAlanase and the sequences inducing cleavage to alanine and proline instead of aspartic and glutamic acid.

mjfitzhenry commented 3 years ago

Seems to work fine. It didn't throw up any errors. Thanks mate.

acesnik commented 3 years ago

Cool, no problem!

I'd recommend checking out the Previous and Next Amino Acid columns in the PSM results file (below is for a trypsin run) for a sanity check to make sure the results make sense. image

-AC