In ococrook/IonMobility: Infrastructure for Ion Mobility enabled mass spectrometry

BiocStyle::markdown()

Package: r Biocpkg("hdxmspro")
Authors: r packageDescription("hdxmspro")[["Author"]]
Last modified: r file.info("hdxmspro.Rmd")$mtime
Compiled: r date()

library(Spectra)
library(BiocStyle)
library(Biostrings)
library(ggplot2)
library(viridis)
library(patchwork)
library(IonMobility)

set.seed(1)

Introduction

This vignette seeks to explain how to process Ion Mobility enabled hydrogen deuterium exchange mass spectrometry data. Ion mobility data includes an additional dimension for peptide separation which reduces the peptide spectra overlap but does also mean that more peptides are resolved increasing the burdon on computational pipelines. The hdxmspro package depends on the IonMobility package which enables generics and methods to handle the additional dimension.

Getting started

We load a small example dataset from the package

data(phosb_test)

We can examine the object. This test object contains 10 spectra. Note that there are a much larger number of spectra than data without the ion mobility dimension.

phosb_test

Additional information located in the spectraData:

spectraData(phosb_test)

Note, the important additional spectra variable ionMobilityDriftTime.

The units here is roughly 0.054 corresponding to the adcPusherFrequency

head(phosb_test$ionMobilityDriftTime)
median(diff(phosb_test$ionMobilityDriftTime)) # estimate adcPusherFrequecy

The separate IonMobility package allow manipulation of this dimension of the data. The following functions work similary to the other filter functions:

head(IonMobility::ionMobilityTime(phosb_test))
exmp <- IonMobility::filterIonMobility(phosb_test, c(0,0.5))
exmp

ococrook/IonMobility documentation built on March 27, 2022, 11:48 a.m.