typo fixes

[cbielow]

Description

X!Tandem's Protein-N-terminal cleavage rules are more flexible than OpenMS' PeptideIndexer allows for.
More specifically, ANY aminoacid (not just 'M') can be cleaved off the protein n-terminus.
This PR makes the behaviour consistent with how X!Tandem calls peptides.

fixes #5755

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[timosachsenberg]

looks simple enough. @jpfeuffer any objections?

[jpfeuffer]

Do we know where it says ANY in Xtandem docs?

[jpfeuffer]

Because it could also just consider X since X matches M

[timosachsenberg]

I think I found some code in the X!Tandem source code that skips * and X at the N-terminus of peptides.

while((m_pSeq[lStart] == '*' || m_pSeq[lStart] == 'X') && lStart < m_lStartMax) ...

[jpfeuffer]

Aha! Nice find. Then the PR won't do much good and an extended strategy is required.

[cbielow]

I think I found some code in the X!Tandem source code that skips * and X at the N-terminus of peptides.

Nice find, Timo.
Can you provide a link to the code?!
And why peptides and not protein?

And all I used to implement the fix was the comment from Ron Beavis here #2497 (comment)

Then the PR won't do much good and an extended strategy is required.

Well, it now could lead to some false positives, if truly only 'X' and 'M' are considered by X!Tandem.
The '*' we must not worry about. It is removed before processing in PeptideIndexer.

[timosachsenberg]

sent link on discord