quantify-methods {MSnbase} | R Documentation

## Quantifies 'MSnExp' and 'Spectrum' objects

### Description

This method quantifies individual `"Spectrum"` objects or full `"MSnExp"` experiments. Current, MS2-level isobar tagging using iTRAQ and TMT (or any arbitrary peaks of interest, see `"ReporterIons"`) and MS2-level label-free quantitation (spectral counting, spectral index or spectral abundance factor) are available.

Isobaric tag peaks of single spectra or complete experiments can be quantified using appropriate `methods`. Label-free quantitation is available only for `MSnExp` experiments.

Since version 1.13.5, parallel quantitation is supported by the `BiocParallel` package and controlled by the `BPPARAM` argument.

### Arguments

`object` | An instance of class `"Spectrum"` (isobaric tagging only) or `"MSnExp"`.
`method` | Peak quantitation method. For isobaric tags, one of, possibly abreviated `"trapezoidation"`, `"max"`, or `"sum"`. These methods return respectively the area under the peak(s), the maximum of the peak(s) or the sum of all intensities of the peak(s). For label-free quantitation, one of `"SI"` (spectral index), `"SIgi"` (global intensity spectral index), `"SIn"` (normalised spectral index), `"SAF"` (spectral abundance factor) or `"NSAF"` (normalised spectral abundance factor). Finally, the simple `"count"` method counts the occurrence of the respective spectra (at this stage all 1s) that can then be used as input to `combineFeatures` to implement spectra counting.
`reporters` | An instance of class `"ReporterIons"` that defines the peak(s) to be quantified. For isobaric tagging only.
`strict` | For isobaric tagging only. If strict is `FALSE` (default), the quantitation is performed using data points along the entire width of a peak. If strict is set to `TRUE`, once the apex(es) is/are identified, only data points within apex +/- width of reporter (see `"ReporterIons"`) are used for quantitation.
`BPPARAM` | Support for parallel processing using the `BiocParallel` infrastructure. When missing (default), the default registered `BiocParallelParam` parameters are applied using `bpparam()`. Alternatively, one can pass a valid `BiocParallelParam` parameter instance: `SnowParam`, `MulticoreParam`, `DoparParam`, ... see the `BiocParallel` package for details.
`parallel` | Deprecated. Please see `BPPARAM`.
`qual` | Should the `qual` slot be populated. Default is `TRUE`.
`pepseq` | A `character` giving the peptide sequence column in the feature data. Default is `"sequence"`.
`verbose` | Verbose of the output (only for `MSnExp` objects).
`...` | Further arguments passed to the quantitation functions.

### Details

`"ReporterIons"` define specific MZ at which peaks are expected and a window around that MZ value. A peak of interest is searched for in that window. Since version 1.1.2, warnings are not thrown anymore in case no data is found in that region or if the peak extends outside the window. This can be checked manually after quantitation, by inspecting the quantitation data (using the `exprs` accessor) for `NA` values or by comaring the `lowerMz` and `upperMz` columns in the `"MSnSet"` `qual` slot against the respective expected `mz(reporters)` +/- `width(reporters)`.

Once the range of the curve is found, quantification is performed. If no data points are found in the expected region, `NA` is returned for the reporter peak MZ.

Note that for label-free, spectra that have not been identified (the corresponding fields in the feature data are populated with `NA` values) or that have been uniquely assigned to a protein (the `nprot` feature data is greater that 1) are removed prior to quantitation. The latter does not apply for `method = "count"` but can be applied manually with `removeMultipleAssignment`.

### Methods

`signature(object = "MSnExp", method = "character", reporters = "ReporterIons", verbose = "logical", ...)`

  For isobaric tagging, quantifies peaks defined in `reporters` using `method` in all spectra of the `MSnExp` object. If verbose is set to `TRUE`, a progress bar will be displayed.

  For label-free quantitation, the respective quantitation methods and normalisations are applied to the spectra. These methods require two additional arguments (`...`), namely the protein accession of identifiers (`fcol`, with detault value `"DatabaseAccess"`) and the protein lengths (`plength`, with default value `"DBseqLength"`). These values are available of the identification data had been collated using `addIdentificationData`.

  An object of class `"MSnSet"` is returned containing the quantified feature expression and all meta data inherited from the `MSnExp` `object` argument.

`signature(object = "Spectrum", method = "character", reporters = "ReporterIons")`

  Quantifies peaks defined in `reporters` using `method` in the `Spectrum` object (isobaric tagging only).

  A list of length 2 will be returned. The first element, named `peakQuant`, is a 'numeric' of length equal to `length(reporters)` with quantitation of the reporter peaks using `method`.

  The second element, names `curveStats`, is a 'data.frame' of dimension `length(reporters)` times 7 giving, for each reporter curve parameters: maximum intensity (`'maxInt'`), number of maxima (`'nMaxInt'`), number of data points defined the curve (`'baseLength'`), lower and upper MZ values for the curve (`'lowerMz'` and `'upperMz'`), reporter (`'reporter'`) and precursor MZ value (`'precursor'`) when available.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb <mail@sebastiangibb.de>

### References

For details about the spectral index (SI), see Griffin NM, Yu J, Long F, Oh P, Shore S, Li Y, Koziol JA, Schnitzer JE. Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat Biotechnol. 2010 Jan;28(1):83-9. doi: 10.1038/nbt.1592. PMID: 20010810; PubMed Central PMCID: PMC2805705.

For details about the spectra abundance factor, see Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. PNAS. 2006 Dec 12;103(50):18928-33. PMID: 17138671; PubMed Central PMCID: PMC1672612.

### Examples

    ## Quantifying a full experiment using iTRAQ4-plex tagging
    data(itraqdata)
    msnset <- quantify(itraqdata, method = "trap", reporters = iTRAQ4)
    msnset

    ## specifying a custom parallel framework
    ## bp <- MulticoreParam(2L) # on Linux/OSX
    ## bp <- SnowParam(2L) # on Windows
    ## quantify(itraqdata[1:10], method = "trap", iTRAQ4, BPPARAM = bp)

    ## Checking for non-quantified peaks
    sum(is.na(exprs(msnset)))

    ## Quantifying a single spectrum
    qty <- quantify(itraqdata[[1]], method = "trap", iTRAQ4[1])
    qty$peakQuant
    qty$curveStats

    ## Label-free quantitation
    ## Raw (mzXML) and identification (mzid) files
    quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "mzXML$")
    identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "dummyiTRAQ.mzid")

    msexp <- readMSData(quantFile)
    msexp <- addIdentificationData(msexp, identFile)
    fData(msexp)$DatabaseAccess

    si <- quantify(msexp, method = "SIn")
    processingData(si)
    exprs(si)

    saf <- quantify(msexp, method = "NSAF")
    processingData(saf)
    exprs(saf)

[Package MSnbase version 2.10.1 Index]