assess_termini {MSnID} | R Documentation

## Checks if the peptide termini conforms with cleavage specificity

### 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 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.

### Usage

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

### Arguments

`object` | An instance of class "MSnID".
`validCleavagePattern` | Cleavage pattern in the form of regular expression.

### Details

N- or C- protein termini are not considered as irregular clevages sites.

### Value

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.

### 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.

### Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

### See Also

`assess_missed_cleavages`

### Examples

    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)

[Package MSnID version 1.28.0 Index]