quantify-methods.Rd: Quantitation of Raw MS Data

In rformassspectrometry/MsQuantitation: Mass Spectrometry Quantitation

Quantitation of Raw MS Data

Description

The quantify() method is the entry point for quantitation of raw mass spectrometry data. The raw data is contained in a Spectra() object while the details and parameters of the quantitation method are defined in a dedicated QuantParam().

Usage

## S4 method for signature 'Spectra'
quantify(object, param, ...)

Arguments

object	An instance of class Spectra().
param	An instance of class QuantParam() that defines the quantitation method.
...	additional parameters controlled parallel processing of the data. See BiocParallel::bplapply() for details.

Value

An instance of QFeatures() with as many assays as there where acquisitions (files) in object.

Examples

## ----------------------------------------
## Labelled MS2 quantitation
## ----------------------------------------

## Test data from the msdata package
f <- msdata::proteomics(pattern = "01.mzML.gz", full.names = TRUE) 
rw <- Spectra(f)

## Quantitation parameters
p <- QuantParam(msLevel = 2L, label = TRUE,
                params = list(reporters = TMT6))
p

quantify(rw, p)

## Simulate data from 2 files
rw <- filterMsLevel(rw, 2L) 
rw <- setBackend(rw, MsBackendDataFrame())

rw$dataOrigin <- sample(c("file1", "file2"),
                        length(rw),
                        replace = TRUE)

quantify(rw, p)

## ----------------------------------------
## Labelled MS3 quantitation
## ----------------------------------------

## Test data from the msdata pakage
basename(f <- msdata::proteomics(pattern = "MS3TMT11", full.names = TRUE))
x <- Spectra(f)

## Quantitation parameters
p <- QuantParam(msLevel = 3L, label = TRUE,
                params = list(reporters = TMT11))
p

quantify(x, p)

rformassspectrometry/MsQuantitation documentation built on June 7, 2022, 5:46 a.m.