Question: Processing .raw files or out.tar files from Mass Spec
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gravatar for K.patel5
6 months ago by
K.patel530
K.patel530 wrote:

Hi Biostars,

I am trying to process the data found in PXD011453. This data contains data files in two formats: .raw and out.tar.

I have been told that there are methods to convert .raw files into .mzML files. Hereafter, I could use standard mass spec approach to process the data found here http://master.bioconductor.org/packages/release/workflows/vignettes/proteomics/inst/doc/proteomics.html.

However, this sounds a bit like a roundabout way to solve the issue. I was wondering if anyone had experience handling .raw files or out.tar files, and if so how was the processing approached?

This is my first go at proteomics so apologies if this is actually a silly question.

Any help or advice would be appreciated.

R mass spec proteomics • 157 views
ADD COMMENTlink written 6 months ago by K.patel530
1

The raw output is specific to each manufacturer and can usually only be handled on Windows. The only software I know of that can handle some raw output files on anything other than windows is maxquant, which works with at least some thermo fisher raw data.

ADD REPLYlink written 6 months ago by Devon Ryan93k

Hi Devon, thank you for the response. The researchers used Orbitrap Fusion Lumos which I believe is a ThemoFisher product. I am using a Linux so I will give Maxquant a look.

ADD REPLYlink written 6 months ago by K.patel530
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