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MALDI support alesur  2024-08-14 02:11
 

Dear Skyline Team,

I recently tested the script MALDISkyLink from C. Ashwood for MALDI support and found that it worked quite well. It essentially duplicates the spectrum and brackets it with background values to add a "fake" time value, allowing Skyline to calculate areas. Could you consider implementing something similar directly into Skyline for the import of MALDI data?

The limitation of this script (in my hands) is that it can only convert MALDI spectra one by one, whereas MALDI users usually have thousands of spots to analyze.

It would be a great addition, as Skyline is a fantastic tool for processing and curating large sample batches. MALDI-MS still has numerous applications in proteomics, glycomics, and the world of small molecules.

Thanks

Best regards
 
 
Nick Shulman responded:  2024-08-14 09:32
Can you send us an example of a MALDI data file (Bruker .d folder?) and your Skyline document?
I have not heard of MALDISkyLink before, but I see that the github project is here:
https://github.com/chrashwood/MALDISkyLink

The program presents a graphical user interface to select a Bruker .d folder and then uses msconvert.exe to convert that to a .mzXML file, and then inserts some additional "<scan>" elements into the XML and then runs msconvert.exe again to produce a new .mzXML file with centroided spectra.

It looks like it would be really easy for us to turn that into a command-line program which you could use as part of a pipeline which converts multiple .d folders.

To send us the Skyline document, you should use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

You should also package your Bruker .d folder into a .zip file as well.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

I have never seen MALDI data before, so I am not sure what would be involved in getting it to work in Skyline without having to add fake spectra to an mzXML file.
I know we have occasionally discussed adding features to support direct infusion data where Skyline would be able to report areas under curves without having to look for any sort of peak, but I do not think we have any immediate plans to do anything like that.
-- Nick
 
Brian Pratt responded:  2024-08-14 09:37

Have you consulted the MALDISkyLink authors? It sounds like it's already very close to meeting your needs, they might have ideas about extending it to handle your scenario. That's probably the swiftest route to victory.

This is similar to dealing with direct injection experiments, another area where Skyline isn't quite suitable because it expects chromatography, and which we've never quite gotten around to. One of the wonderful things about Skyline is its openness, where the community can contribute solutions that our small team hasn't gotten to yet (and may never get to).

Thanks for using the Skyline support board,

Brian Pratt
 
Chris Ashwood responded:  2024-08-15 02:24

Hi alesur,

I'm the MALDISkyLink author and it's great to hear that someone else has found it useful. That said, it is generally available "as-is" as I haven't worked on it in three years and it was developed specifically for the data on our Bruker Ultraflextreme (positive mode, single "scan" per .d folder). I've just provided a license file (Apache 2.0) on the repository so you can modify the code if you have the capacity to do so.

If you could follow the instructions provided by Nick Shulman, I can take a look at the data structure and I might be able to implement a quick fix to allow you to convert 1000's of files in a single shot.

Another caveat I have to give is that it is more qualitative than quantitative because of the way the data are processed (fake scans to determine background noise). We've submitted a manuscript using it (minor part of the publication) so it might be officially published sooner than later.

Cheers,
Chris
 
alesur responded:  2024-08-16 01:55

Hello,

Thank you to everyone for your responses.

In the attached Zip file, you will find the following:

  • The Skyline file
  • The Bruker Ultraflex raw file
  • The same raw file converted to mzXML
  • The file converted by MALDISkyLink

It is simply a mixture of permethylated O-glycans, and I added a few compositions in Skyline for testing purposes. With MALDI or infusion, you could even get Skyline to work with a single point and report peak height instead of areas, that would make Skyline natively compatible with MALDI without this workaround.

@Chris, thank you for making your script available. I believe it should be quantitative as long as the time between the two duplicated spectra remains the same. The value of the background is negligible compared to the "real" background in my spectrum, so it acts as a quasi-zero value. We should be careful with compounds of low S/N ratios. I think the quantitative aspect can easily be tested with some calibration curves.

Antoine
 
Chris Ashwood responded:  2024-08-18 19:18

Hi Alesur,

The files provided all appear to only have one scan/spot in them (K24). Do you have any files with more than one spot? I'll need one of those files to ensure that we can extract the data of multiple spots from a single file.

Cheers,
Chris
 
alesur responded:  2024-08-19 08:06

Hi Chris,

Thank you for your help.
Sure, please find the files of attached 3 samples.

Cheers
Antoine