assess_missed_cleavages {MSnID} | R Documentation

## 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.

### Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

### See Also

`assess_termini`

### Examples

    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)

[Package MSnID version 1.24.0 Index]