readMaxQuantProtGroups: Reading MaxQuant Output

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

Reads in "proteinGroups.txt" output (or its compressed version) as MSnSet.

Usage

readMaxQuantProtGroups(path, quantType, verbose = 1)

Arguments

path	character path to the folder containing "proteinGroups.txt file". It should be in "raw files folder/combined/txt"
quantType	character Defines pattern what type of column to use for quantificaiton. E.g. "LFQ intensity" or "Ratio H/L normalized".
verbose	numeric controls the text output

Details

As feature data, only first 12 columns and iBAQ columns are used. Features are based on the genes. In case of multiple proteins matching the same gene, only the one with the highest iBAQ value is returned.

Value

MSnSet object

Note

The "proteinGroups.txt" file can be compressed (gzip) to save space.

It looks like the convention for column naming in MaxQuant is type of quantification followed by sample name separated by space. E.g. "LFQ intensity Sample1" or "Ratio H/L normalized Control33". In quantType you need to specify the full first component in the name that defines the type of quantification.

iBAQ option must be enabled in MaxQuant analysis because it is used to resolve ambiguity between two proteins matching one gene.

Examples

# label-free data
m <- readMaxQuantProtGroups(system.file("extdata/MaxQuant",
                                         package="vp.misc"),
                            quantType="LFQ intensity")
exprs(m) <- log2(exprs(m))
exprs(m) <- sweep(exprs(m), 1, rowMeans(exprs(m), na.rm=TRUE), '-')
image_msnset(m)

# O18/O16 data
m <- readMaxQuantProtGroups(system.file("extdata/MaxQuant_O18",
                                         package="vp.misc"),
                            quantType="Ratio H/L normalized")
exprs(m) <- log2(exprs(m))
exprs(m) <- sweep(exprs(m), 1, rowMeans(exprs(m), na.rm=TRUE), '-')
image_msnset(m)

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.