Regarding the error at conversion of .raw file to mzML files

[ARPITA TIWARI]

Hello everyone, 

I have attached the following error below I have installed the TPP in M1 MAC os with the help of source link. Now I am trying to convert .raw file into mxML. Somehow, it isn"t happening.

I will be grateful if anyone an solve this problem. 

Thank you 

Best regards

Arpita

   

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[David Shteynberg]

Hello Arpita,

Thanks for your question.  Conversion from RAW happens with the help of Thermo dll libraries which only function on windows.  To process proteomics data with TPP on a Mac you have to start with mzML or mzXML data and convert the data on another computer.

Best,

David

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[ARPITA TIWARI]

Dear David,

Okay will do that, thank you so much for your response.

Best regards

Arpita

To view this discussion visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9-kWANEOMqzd8L2UzAWDZdaLYTkCSXEZP1yUx9WxPGJg%40mail.gmail.com.

[ARPITA TIWARI]

Sorry to disturb you but can I know why is it not possible on Mac? Why does Thermo libraries work in windows only? Is there any other solution ?

Best regards

Arpita 

[David Shteynberg]

Hello Arpita,

Unfortunately, DLL files are Windows specific and do not function on Mac.  Whether or not Thermo is planning on providing RAW data access libraries that function on Mac is a question for Thermo, but I suspect this is not a top priority for most customers.  I hope you are able to convert your data to open formats on another computer and then continue using the TPP on your Mac.

Best,

-David

To view this discussion visit https://groups.google.com/d/msgid/spctools-discuss/CAN-RRUeGH%3D%3D949HnZUD3LqMs9Ezo0_ZARn1N0xo5WvWogE6Vug%40mail.gmail.com.

[Robert Winkler]

Hi, you can convert the raw data to mzML on any computer that runs docker. E.g. I use this strategy to convert Thermo files on a Linux System. The chambm container simulates a Windows system and contains the necessary vendor libraries. My command looks like this from the command line:

docker run -it -v /home/antix/Downloads/ThermoDDA:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/*.raw

Best, Robert

[ARPITA TIWARI]

Okay I will try to do it.  Thank you very much. 

Best

Arpita

To view this discussion visit https://groups.google.com/d/msgid/spctools-discuss/0d861eaa-3d4c-4733-b4f0-f8ffa92a684dn%40googlegroups.com.

[Sebastian Paez]

Hi there!

I have not been able to make pwiz-docker run in a mac computer (at least with M-series macs) but was able to use thermorawfileparser.

https://github.com/compomics/ThermoRawFileParser 

LMK if either of those options work for you!

Best

-Sebastian

[ARPITA TIWARI]

Thank you will look into it. 

Best regards 

Arpita

To view this discussion visit https://groups.google.com/d/msgid/spctools-discuss/f873c5d6-0e19-41a5-b248-906435fe7a2bn%40googlegroups.com.