In rformassspectrometry/MsBackendTimsTof: Mass spectrometry Data Backend for Bruker TimsTOF Files

BiocStyle::markdown()

Package: r Biocpkg("MsBackendTimsTof")
Authors: r packageDescription("MsBackendTimsTof")[["Author"]]
Compiled: r date()

library(Spectra)
library(BiocStyle)

Introduction

The r Biocpkg("Spectra") package provides a central infrastructure for the handling of Mass Spectrometry (MS) data. The package supports interchangeable use of different backends to import MS data from a variety of sources (such as mzML files). The r Biocpkg("MsBackendTimsTof") package adds support for Bruker TimsTOF raw data files. This vignette shows how, and which data can be retrieved from such files.

Installation

The package depends on the OpenTIMS C++ library to access data in timsTOF Pro data format (TDF) which is provided by the opentimsr R package. The MsBackendTimsTof package can be installed with:

BiocManager::install("RforMassSpectrometry/MsBackendTimsTof")

To get some variables from the data files an additional library from the manufacturer is needed. This library can be downloaded with:

so_folder <- tempdir()
library(opentimsr)
so_file <- download_bruker_proprietary_code(so_folder)

This downloads the shared library to a temporary folder. Note however that at present this shared library is only available for Windows and Linux (i.e. no macOS support). Next, to use this library, it has to be registered with the opentimsr package:

setup_bruker_so(so_file)

These steps would be necessary for every new R session. To avoid that, it is suggested to copy the downloaded shared library above to a directory on the computer and to define an environment variable called TIMSTOF_LIB that defines the full path where this file is located (i.e. a character string defining the full file path with the file name). This variable can either be defined system wide, or within the .Rprofile file. An example entry in a .Rprofile could for example be:

options(TIMSTOF_LIB = "/home/jo/lib/libtimsdata.so")

Accessing data from Bruker TimsTOF files

The r Biocpkg("MsBackendTimsTof") package adds support for Bruker TimsTOF files to Spectra-based analysis workflows. Below we load the package and in addition fetch the required shared library and store that to a temporary folder.

library(MsBackendTimsTof)

## Load the opentimsr package and download and register the shared library
library(opentimsr)
so_folder <- tempdir()
so_file <- download_bruker_proprietary_code(so_folder, method = "wget")
setup_bruker_so(so_file)

As detailed in the installation section, the code to download the shared library would only be necessary once, if the path to this file is defined in a environment variable TIMSTOF_LIB.

We next load the TDF test file which is bundled within this package.

fl <- system.file("ddaPASEF.d", package = "MsBackendTimsTof")

be <- backendInitialize(MsBackendTimsTof(), fl)

In a real use case, we would however directly load the data into a Spectra object:

sps <- Spectra(fl, source = MsBackendTimsTof())
sps

We thus have access to all spectra variables within the file:

spectraVariables(be)

And the full data can be retrieved with spectraData:

all <- spectraData(be)
all

The data is organized by individual spectra, all spectra measured within the same frame have the same value in the spectra variable "frameId". Spectra variable "inv_ion_mobility" provides the inverse ion mobility information. This variable is available as a spectra variable, but also as a peaks variable along with e.g. "tof". Available peaks variables can be listed with the peaksVariables function.

peaksVariables(sps)

Below we subset the backend to a range of spectra and extract their peaksData.

sps_sub <- sps[224:227]
peaksData(sps_sub, columns = c("mz", "intensity", "tof", "inv_ion_mobility",
                               "retention_time")) |> as.list()

Note however that both the "inv_ion_mobility" and "retention_time" have the same value for all peaks in each spectrum. Thus, these variables should be accessed not through peaksData, but through spectraData or using the $ operator or the dedicated rtime function. Below we extract the inverse ion mobility values and display the first 6 of them.

head(sps$inv_ion_mobility)

The MsBackendTimsTof is a on-disk backend, hence reading peaks and spectra variables from the original data file(s) upon request. Modifying spectra variables within the raw data files is not possible (and also not desired), but, by directly extending the MsBackendCached backend from the r Biocpkg("Spectra") package MsBackendTimsTof supports changing or adding spectra variables by caching them locally within the object. Below we add a new spectra variable to the object.

sps$new_variable <- seq_along(sps)

This new variable is now available within the object and can be extract like any other spectra variable.

spectraVariables(sps)
sps$new_variable |> head()

Analogously it is also possible to change existing spectra variables. Below we add a value to each retention time.

rtime(sps) |> head()
sps$rtime <- rtime(sps) + 10
rtime(sps) |> head()

Session information

sessionInfo()

rformassspectrometry/MsBackendTimsTof documentation built on Oct. 21, 2023, 4:19 p.m.