N-term enzyme miss-cleavage

[cpaul32015]

No description provided.

[cpaul32015]

In another case where it seems more like a bug is where I searched with a custom enzyme lysarginase which cleaves N-term to 'K' and 'R', even when I set the allowed MC to 3 I am actually getting peptides up to 5 MC (counting K and R as miss-cleaved sites). Could this issue be something to do with how the algorithm treats proteases cleaves on the N-term to the AA?

[jke000]

Thanks for reporting this. I just spent about 30 minutes looking into this and there is a bug with the logic of counting missed cleavages; at first glance appears to be an issue with N-term enzymes/cleavages. I'll spend time on Monday addressing this and comment more at that time.

[cpaul32015]

Thank you for the quick response over the weekend! I want to correct about my initial question, turned out I mistakenly counted the cleavage site of AspN to be before 'N' but it should be before 'D', I got that corrected and the MCs for that search made sense now.
The custom lysarginase is still reporting results with 5 MCs when I set to use 3 MCs in the parameter file, it will be great if you can look into it further if it is indeed a bug.

Have a great weekend!

[jke000]

Zixiang, I implemented the little fix for this issue but I want to do a few additional tests just to confirm all is well. If you're able to test on your lysarginase dataset, I have patched Comet binaries here that you can download. It would be reassuring to hear that this addresses the issue in your dataset.

[cpaul32015]

Hi Jimmy,

Thanks for so quickly addressing the issue, is the current state of Comet search affecting the counting of all N-term enzymes or just the custom ones? From my previous tests it appears that AspN in combination with trypsin worked correctly but the custom lysarginase was having issue.

[jke000]

The bug affected properly counting all N-term enzyme missed cleavages.

[jke000]

I'm going to close this issue which is addressed with commit d7f202b and will be included in the next release, whenever that might be.