Convert mgf to mzML/mzXML

[Panos Ioannidis]

Hello,

Does anyone know how to convert mgf files to mzML/mzXML?

Thanks,

Panos

[Michael Hoopmann]

I would use msconvert from proteoWizard, It's part of the TPP. The command line would look like this:

>msconvert yourFile.mgf --mzML

you can also simply type "msconvert" for examples of the many conversion options available to you.

Cheers,

Mike

[Panos Ioannidis]

Thanks a lot Mike!

And what if I want to convert RAW files to mzML in Linux? The Linux version of ProteoWizard tools says that they cannot process vendor files (such as RAW). Is there an alternative? I have already tried using msconvert with wine but didn't work? Is there a conversion tool running natively in Linux?

Panos

[Michael Hoopmann]

No, there isn't a native tool for Linux that reads vendor formats. Unfortunately, vendor formats are proprietary and requires the vendor drivers to access those files and convert them. All of those drivers are Windows only, as the vendors have decided that is their platform of choice. Thermo will eventually release a Linux compatible driver set for Mono, maybe you can even get your hands on the development version - but it will only read the file. Converting it to another format will require additional coding or interfacing with ProteoWizard.

One possible solution would be to create a Windows virtual machine for converting vendor formats. It can be fired up inside Linux, then convert the vendor files to mzML using msconvert from ProteoWizard, copy the mzML files back to your Linux filesystem, and wind down the VM.

Cheers,

Mike

[Panos Ioannidis]

Yes, I did think of setting up a Windows VM for such conversions, and maybe it's unavoidable after all...

Thanks a lot for your time!

P

[Antonio Ortega]

Hi Panos

You can give it a try with https://github.com/compomics/ThermoRawFileParser . It supports raw -> mgf  conversion in Linux, and a raw -> mzML conversion is on the making. I have successfully been able to extract mgf files from RAW files in Linux with this tool.

The instructions for how to set it up are given in the README.md file. If you experience difficulties, have a look at the issues (open and closed), or open a new one ;)

Best

Antonio

[Panos Ioannidis]

Thanks Antonio! I will give it a try.

[Adam Rabalski]

Hi Mike,

Do you know if this has changed recently? I see that Thermo has a RawFileReader that they say is compatible with linux now http://planetorbitrap.com/rawfilereader#.W19raqdKi71 Is this the linux compatible driver you speak of? Is there a msconvert version that can take the vendor library from thermo and convert raw -> mzML in linux? Or is this still only possible through mono or a windows vm? How does your group at ISB handle this and which VM setup do you recommend?

Best,

Adam

[Michael Hoopmann]

Hi Adam,

Yes, that is the linux compatible driver. Specifically, it works through Mono. However, I'm not sure if any existing converters have been updated to make use of it. msconvert is maintained by ProteoWizard, and it might be best to see if they have a linux version that uses those drivers. I am not sure what VM we use for our msconvert via linux, but perhaps someone else on this board knows.

Cheers,

Mike

[Adam Rabalski]

Hi Mike,

Thanks for the clarification. I've sent the folks at ProteoWizard an e-mail. Anything I learn I'll post in the forum.

Best,

Adam

[Adam Rabalski]

Never received a response back from the folks at ProteoWizard. If anyone else has learned of anything new, please share!

[Adam Rabalski]

Never got a reply directly back but the post was answered on the sourceforge site:

https://sourceforge.net/p/proteowizard/mailman/message/36379927/

Short answer is no long answer is it would take a rewrite to implement on linux.

[Chambers, Matthew]

Hi Adam,

Try the Docker container here:
https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses/
Use the "x64" tag.

It uses Wine to run the Windows version of msconvert. It works for most vendor formats:
https://github.com/phnmnl/container-pwiz/issues/8#issuecomment-408958177

-Matt

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