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diogobor / Scout

MS-cleavable search engine that enables interactomic analysis by identifying tandem mass spectra of cross-linked peptides.
MIT License
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Can we set both Thiol- and sulfenic acid- form in the HeavyFragment? #1

Closed helloworld1631 closed 1 year ago

helloworld1631 commented 1 year ago

Hi,

I am wondering if can set both unsaturated thiol and sulfenic acid as the heavy fragment modification. Do you think it will increase the identification number?

Thank you!

diogobor commented 1 year ago

Hello,

The current architecture of Scout does not allow to set both unsaturated thiol and sulfenic acid as the heavy fragment modification. For the current version, my idea would be performing two searches: 1) setting up the unsaturated thiol as heavy frag modification and 2) setting up the sulfenic acid as heavy frag modification. At the end, merge both results.

In terms of increasing the identification number, I don't think this strategy will significantly increase the number of IDs, since the tendency to observe neutral losses in the most current mass spectrometers is smaller, mainly when HCD is used to acquire the dataset.

Best, Diogo

helloworld1631 commented 1 year ago

Thanks for your suggestion, Diogo! I will have a try.

Thank you!