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baynec2 / mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data
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real sequence vs match sequence #4

Closed baynec2 closed 6 months ago

baynec2 commented 6 months ago

Think about what to do about this. Should I alter it ? Or just leave it?

Briefly, it is the way it is because methionines in the peptide library were replaced with norleucines (which have the same side chain as methionine with the S converted to C but are the same exact mass as L). This was done because methionines can be oxidized either singly or doubly which could pose problems, but n should be similar to M in the way it is recognized by proteases.

Peaks recognizes n as L, and then we change it to a M in the code because that is all IceLogo can handle. Then we know that the M is actually a n, and change it later in illustrator.

baynec2 commented 6 months ago

Decided to just leave the way it is for now as it doesn't seem like that big of an issue. Will reopen in the future if it comes up again