assess_termini: Checks if the peptide termini conforms with cleavage...
In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description Usage Arguments Details Value Warning Author(s) See Also Examples

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 possesses amino acid cleavage specificity.

This function checks if peptide termini are as expected given the enzymatic/chemical cleavage specificity. The default value for validCleavagePattern is [KR]\.[^P], which corresponds to trypsin.

1	assess_termini(object, validCleavagePattern="[KR]\\.[^P]")

`object`	An instance of class "MSnID".
`validCleavagePattern`	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 1 and 2, correspondingly.

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.

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

assess_missed_cleavages

data(c_elegans)
# adding column numIrregCleavages 
# containing count of irregularly cleaved termini
msnidObj <- assess_termini(msnidObj, validCleavagePattern="[KR]\\.[^P]")
# check the distribution
table(msnidObj$numIrregCleavages)