calculate.emPAI: 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.

Value

Named numeric vector of emPAI values.

Details

The formula is $$emPAI = 10^{\frac{N <- {observed}}{N <- {observable}}} -1$$ 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.

References

Ishihama Y, et al., Proteomics (2005)

Examples

Run this code

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

Run the code above in your browser using DataLab