bioconductor-msdatahub

name	bioconductor-msdatahub
description	The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

MsDataHub

Workflows

Standard Workflow

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

library(MsDataHub)
library(Spectra)
library(QFeatures)

# 1. Load raw MS data (TripleTOF DDA) and create a Spectra object
f_dda <- PestMix1_DDA.mzML()
s_dda <- Spectra(f_dda)

# 2. Load DIA-NN label-free DIA data and read into QFeatures
lfdia <- read.delim(MsDataHub::benchmarkingDIA.tsv())
qf <- readQFeaturesFromDIANN(lfdia)

Note: Inputs are cached file paths retrieved from MsDataHub accessor functions; outputs are Spectra or QFeatures objects containing mass spectrometry data.

When to Use