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
CNBr also possess amino acid cleavage specificity. In real-world
not every cleavage site get cleaved during the sample processing.
Therefore settings of MS/MS search engines quite often explictly
allow up to a certain number missed clevage sites per peptide sequence.
This function counts the number of missed cleavages in peptide
sequence given the endoprotease cleavage motif in the form of
regular expression. The default value for
[KR](?=[^P$]), which corresponds to trypsin.
An instance of class "MSnID".
Cleavage pattern in the form of regular expression.
Returns an instance of "MSnID" class with additional column "numMissCleavages"
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
1 2 3 4 5 6
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.