Instruction needed

[witszymanski]

Hi!

In the manuscript you write:

Thus, MsQuality supports a large variety of data input formats (ranging from mzML, mzXML, CDF, MGF, MSP to some raw vendor file formats, such as Bruker TimsTOF and Thermo raw files)

Can you provide some instruction on how to load the .raw files and .d folders into an object? I couldn't find any info about this.

Greets

Witek

[jorainer]

For .raw files you would need to use the MsBackendRawFileReader and for .d files the MsBackendTimsTOF package.

To import/represent MS data from these raw data formats using Spectra you would need to use e.g.

library(Spectra)
library(MsBackendTimsTof)

sps <- Spectra("data/TimsTOF/Urine 1to1 PASEF pos_16_2_528.d/", source = MsBackendTimsTof())
sps
MSn data (Spectra) with 1522547 spectra in a MsBackendTimsTof backend:
          msLevel precursorMz  polarity
        <integer>   <numeric> <integer>
1               1          NA         1
2               1          NA         1
...           ...         ...       ...
1522546         1          NA         1
1522547         1          NA         1
 ... 35 more variables/columns.
 Use  'spectraVariables' to list all of them.

so, once you have the data imported through Spectra respectively the backend you can use MsQuality on that.

Note that MsBackendTimsTof depends on the opentimsr which was however removed from CRAN, so you would need to install first opentimsr, then MsBackendTimsTof. Also, note that the MsBackendTimsTof is currently in developmental status.

remotes::install_github("michalsta/opentims", subdir="opentimsr")
remotes::install_github("RforMassSpectrometry/MsBackendTimsTof")