assess_missed_cleavages: Counts the missing cleavage sites within the peptides sequence

Description

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 missedCleavagePattern is [KR](?=[^P$]), which corresponds to trypsin.

Usage

assess_missed_cleavages(object, missedCleavagePattern="[KR](?=[^P$])")

Arguments

object

An instance of class "MSnID".

missedCleavagePattern

Cleavage pattern in the form of regular expression.

Value

Returns an instance of "MSnID" class with additional column "numMissCleavages"

Warning

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) where msnid is your "MSnID" instance.

Examples

Run this code

data(c_elegans)
# adding column numMissCleavages containing count of missed cleavages
msnidObj <- assess_missed_cleavages(msnidObj, 
                                    missedCleavagePattern="[KR](?=[^P$])")
# check the distribution
table(msnidObj$numMissCleavages)