Bottom-up proteomics approaches utilize endoproteases or chemical agents
to digest proteins into smaller fragments called peptides.
The enzymes recognize short amino acid motifs
and cleave along the peptide bonds. Chemical agents such as
possesses amino acid cleavage specificity.
This function checks if peptide termini are as expected given the
enzymatic/chemical cleavage specificity.
The default value for
[KR]\.[^P], which corresponds to trypsin.
An instance of class "MSnID".
Cleavage pattern in the form of regular expression.
N- or C- protein termini are not considered as irregular clevages sites.
Returns an instance of "MSnID" class with additional
column "numIrregCleavages". If both termini conforms with
cleavage specificity, then value is
0, if one or two
termini are irregular then the values are
If the "MSnID" instance does not contain "peptide" column in MS/MS results
table then there will be an error.
E.g. you can check this by
"peptide" %in% names(msnid)
msnid is your "MSnID" instance.
Vladislav A Petyuk firstname.lastname@example.org
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