calculate.emPAI: emPAI approximate abundance calculations.

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

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"))

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to isobar (v 1.22.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    paste0

Loading required namespace: OrgMassSpecR

  P00450   P13635   Q61147 
2.096771 4.092096 2.919407 
Warning message:
system call failed: Cannot allocate memory 

isobar documentation built on Nov. 8, 2020, 7:48 p.m.