Extract method file from Thermo Raw file Josh Baeza  2023-10-25 08:51
Hello Skyline Team,

Would it be possible to extract the method file path and name (C:\Path\To\method.meth) from a Thermo .raw file and export this field in the report?

Brian Pratt responded:  2023-10-25 11:55
As a starting point, is that information expressed when the file is converted to mzML with msconvert? Sounds like a random question, but Skyline and msconvert share the same reader libraries so this is an easy way to know if that kind of metadata is likely to make it through to Skyline.

Thanks for using the Skyline support board,

Brian Pratt
Josh Baeza responded:  2023-10-25 19:00
Thanks for your reply. I looked through an mzML file and did not find anything associated with the method file name. However, the method file name is saved in the raw file and can be found by navigating to Right click/View/Report/Sample Information (see screenshot). I just don't know how to extract this information.

Thanks again.
Brian Pratt responded:  2023-10-26 09:24
Not sure what software that is, but the information you can access there isn't necessarily embedded in the file itself. That software is presumably managing a database that includes the file as part of a larger superset of metadata. Hard to say from a screenshot.

If you can provide an example file we could dig through it with a binary editor and see if we find any evidence of that information in there.
Josh Baeza responded:  2023-10-30 08:25
Hi Brian,

I attached a raw file as well as some screen shots of how I look up the Instrument Method name. I'm using a raw file that I downloaded from Panorama since I can't upload any work-related files. However, since the file is from Panorama, would this mean the method file name is embedded in the raw file itself?

Thanks again for your help.
Josh Baeza responded:  2023-10-30 08:29
it seems like the raw file wasn't uploaded. Is there another way to send it?
Brian Pratt responded:  2023-10-30 09:27
You can upload to http://skyline.ms/files.url - or anything else that's convenient for you, just let me know.

Josh Baeza responded:  2023-11-01 09:55
Thanks for sending the upload link. I uploaded a raw file. It is called "20200828_QEHFX_lkp_pSILAC-DIA_btz_LIB1_400-500MZ_144.zip"

Brian Pratt responded:  2023-11-01 12:51
OK, I think there's hope - using a binary editor I can see that the method file is "D:\dia\QEHFX_LIB_GPF1_400-500_4mzol_centroid_lockmass.meth".

The next question is whether or not the reader library that Thermo provides can express that information.

After that the question is how is that best represented in the mzML framework that Skyline shares with msconvert.

Hopefully Matt Chambers can weigh in on that.
Will Thompson responded:  2023-11-01 13:21
Sort of the same...but I'm actually interested to know if Skyline would be able to keep a record of the method parameters from the raw file so that they can be read or displayed. There is a "header" file in Thermo raw data, for instance, that contains all the instrument acquisition variables. One idea is that Skyline could display this 'header' information in a window (like you do for spectrum viewing)...except the file is small enough so perhaps it just lives in the Skyline doc and does not need read-access to the *.raw file all the time. Having this information at your fingertips could allow you to look at someone's data acquisition parameters without leaving skyline.


Brian Pratt responded:  2023-11-02 11:11
Probably the best we could do is just present a big text blob, since every instrument has a different set of possible parameters, but that would probably still be useful. But that much could probably be abstracted across the wide variety of instruments supported by Skyline.
Matt Chambers responded:  2023-12-13 08:27
Sorry I didn't see this question before. Both the method filename and the method itself can be extracted from Thermo RAW. One or both are available from most other vendor formats as well. I'm not sure ProteoWizard/msconvert should always be exporting the entire method (as a text blob like Brian suggests) to the mzML by default, but opting into it seems totally reasonable. And always exporting the method filename when it's available seems reasonable as well. Not sure there's a CV term for it though.