calculate.emPAI {isobar} | R Documentation

## emPAI approximate abundance calculations.

### Description

The Exponentially Modified Protein Abundance Index (emPAI) is a label free quantitative measure of protein abundance based on protein coverage by peptide matches. The original publication is Ishihama Y, et al., Proteomics (2005).

### Usage

    calculate.emPAI(protein.group, protein.g = reporterProteins(protein.group), normalize = FALSE,
                    observed.pep = c("pep", "mod.charge.pep"), use.mw = FALSE, combine.f = mean,
                    ..., nmc = 0, report.all = FALSE)
    n.observable.peptides(...)
    observable.peptides(seq, nmc = 1, min.length = 6, min.mass = 600, max.mass = 4000,
                        custom = list(code = c("B", "Z", "J", "U"),
                                      mass = c(164.554862, 278.61037, 213.12392, 150.953636)), ...)

### Arguments

`protein.group` | ProteinGroup object. Its `@proteinInfo` slot `data.frame` must contain a `sequence` column to calculate the number of observable peptides per protein.
`protein.g` | Protein group identifiers.
`normalize` | Normalize to sum = 1?.
`observed.pep` | What counts as observed peptide?
`report.all` | TOADD
`use.mw` | Use MW to normalize for protein size
`combine.f` | How to handle proteins seen only with shared peptides?
`seq` | Protein sequence.
`nmc` | Number of missed cleavages.
`min.length` | Minimum length of peptide.
`min.mass` | Minimum mass of peptide.
`max.mass` | Maximum mass of peptide.
`custom` | User defined residue for `Digest`.
`...` | Further arguments to `observable.peptides`/`Digest`.

### Details

The formula is

emPAI = 10^(N_observed/N_observable) -1

N_observed is the number of observed peptides - we use the count of unique peptide without consideration of charge state. N_observable is the number of observable peptides. Sequence cleavage is done using `Digest`.

### Value

Named numeric vector of emPAI values.

### Author(s)

Florian P Breitwieser

### References

Ishihama Y, et al., Proteomics (2005)

### See Also

`Digest`, `proteinInfo`, `getProteinInfoFromUniprot`, `calculate.dNSAF`, `ProteinGroup`

### Examples

    data(ibspiked_set1)
    protein.group <- proteinGroup(ibspiked_set1)
    calculate.emPAI(protein.group,protein.g=protein.g(protein.group,"CERU"))

[Package isobar version 1.28.1 Index]