TMTPurityCorrection

Installation

library(devtools)
install_github("GoldfarbLab/TMTPurityCorrection")

Usage

# Extract uncorrected reporter intensities from MaxQuant results
data <- read_tsv("evidence,txt") %>% select(matches("Reporter intensity \\d+"))
# Read in lot-specific impurity file
impurities <- read_csv("VJ309267.csv")
# Correct impurities
correctedIntensities <- correctTMTproImpurities(data, impurities)

Creating a lot-specific impurity file

1. Find the data sheet for your lot at the bottom of: https://www.thermofisher.com/order/catalog/product/A44520#/A44520
2. Create a csv file in the same format as data-raw/VJ309267.csv, which is created from the product sheet below.
3. Note, the "extra" column's value is the row sum of impurities that don't correspond to a label.