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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Seeking advices about data importing #717

Open Babyfaceout opened 8 months ago

Babyfaceout commented 8 months ago

I need some advice about data importing，It's very important to me. here is the original text from xcms guidline: xcms supports analysis of any LC-MS(/MS) data that can be imported with the Spectra package. Such data will typically be provided in (AIA/ANDI) NetCDF, mzXML and mzML format but can, through dedicated extensions to the Spectra package, also be imported from other sources, e.g. also directly from raw data files in manufacturer’s formats. I wonder if there are any suggestions about dedicated extensions. I have searched for a long time, but I have found nothing. I am looking forward to your reply!

stanstrup commented 8 months ago

It's probably easier to help you if you state what you want to do.

Babyfaceout commented 8 months ago

Thank you for your reply！ I want to use raw data files in manufacturer’s formats without msconvert. because I can't install docker in my linux. I wouder if there are any packages or modules can convert raw file to mzxml from manufacturer’s formats, or just parsing raw data files in manufacturer’s formats directly before using xcms. looking forward to your reply! yours sincerely, edison

sneumann commented 8 months ago

Which vendor ? Yours, Steffen

Babyfaceout commented 7 months ago

Which vendor ? Yours, Steffen

thermo QE HFX yours sincerely,

jorainer commented 7 months ago

Thermo raw files can be imported/used with the MsBackendRawFileReader.

With that you should be able to read MS data from the raw files. See the documentation from the package for more information.

With xcms, you need to load the data as an MsExperiment. You should be able to do that with the code below.

library(xcms)
library(MsExperiment)
library(MsBackendRawFileReader)

mse <- readMsExperiment(fls, source = MsBackendRawFileReader())

where fls should be the file names of your raw files. If that works you should be able to work directly with the raw files.

Note that I've never tried it and I don't know how complicated it is to get the MsBackendRawFileReader installed and working. Maybe installing Proteowizard and using its (gui) msconvert functionality to convert raw to mzML might turn out to be easier.