iPQF {MSnbase} | R Documentation

## iPQF: iTRAQ (and TMT) Protein Quantification based on Features

### Description

The iPQF spectra-to-protein summarisation method integrates peptide spectra characteristics and quantitative values for protein quantitation estimation. Spectra features, such as charge state, sequence length, identification score and others, contain valuable information concerning quantification accuracy. The iPQF algorithm assigns weights to spectra according to their overall feature reliability and computes a weighted mean to estimate protein quantities. See also `combineFeatures` for a more general overview of feature aggregation and examples.

### Usage

    iPQF(
      object,
      groupBy,
      low.support.filter = FALSE,
      ratio.calc = "sum",
      method.combine = FALSE,
      feature.weight = c(7, 6, 4, 3, 2, 1, 5)^2
    )

### Arguments

`object` | An instance of class `MSnSet` containing absolute ion intensities.
`groupBy` | Vector defining spectra to protein matching. Generally, this is a feature variable such as `fData(object)$accession`.
`low.support.filter` | A `logical` specifying if proteins being supported by only 1-2 peptide spectra should be filtered out. Default is `FALSE`.
`ratio.calc` | Either `"none"` (don't calculate any ratios), `"sum"` (default), or a specific channel (one of `sampleNames(object)`) defining how to calculate relative peptides intensities.
`method.combine` | A `logical` defining whether to further use median polish to combine features.
`feature.weight` | Vector `"numeric"` giving weight to the different features. Default is the squared order of the features redundant -unique-distance metric, charge state, ion intensity, sequence length, identification score, modification state, and mass based on a robustness analysis.

### Value

A `matrix` with estimated protein ratios.

### Author(s)

Martina Fischer

### References

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Fischer M, Renard BY. Bioinformatics. 2016 Apr 1;32(7):1040-7. doi:10.1093/bioinformatics/btv675. Epub 2015 Nov 20. PubMed PMID:26589272.

### Examples

    data(msnset2)
    head(exprs(msnset2))
    prot <- combineFeatures(msnset2,
                            groupBy = fData(msnset2)$accession,
                            method = "iPQF")
    head(exprs(prot))

[Package MSnbase version 2.20.1 Index]