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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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Allow for customizable proteases (like mods) #402

Closed rmillikin closed 7 years ago

rmillikin commented 7 years ago

AspN protease selection currently only generates theoretical peptides cleaved at D, but could also include C and Q: The endoproteinase AspN cleaves primarily at amino side of aspartate residues and cysteic acid residues that result from the oxidization of cysteine residues, generating a limited number of peptide fragments. Cleavage can also occur at glutamic residues; however, the rate of cleavage at the glutamyl residues is significantly lower than the rate of cleavage at the aspartic acid residues.

I am curious as to how many PSMs we are mis-assigning when using other proteases because we are not including these known observed cleavages in our search space.

rmillikin commented 7 years ago

Woops! This is Zach Rolfs on Rob's account, since it was logged in on Artemis. Sorry Rob!

stefanks commented 7 years ago

You can edit the proteases file to add a custom protease with any digestion sites. Customizing cleavage taking modifications into account is discussed here: https://github.com/smith-chem-wisc/MetaMorpheus/issues/404