Automatically import transitions list from Waters triple quandrupoles RAW files

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Automatically import transitions list from Waters triple quandrupoles RAW files gioele visconti  2021-08-20
 

Good morning,

First of all, thank you for your work. I really appreciate the program and its multi-platform versatility.

I would like to suggest if the MRM transitions list that are contained into the RAW files of triple quadrupoles instrument (see attached pictures) can be automatically imported into Skyline. To my knowledge, this function is not present and the user need to manually create a transition list.
I am currently using a Waters instrument (TQ-XS) and exporting the MRM transitions is very laborious and not automatable.

Thank you and best regards.

Gioele Visconti

 
 
Brian Pratt responded:  2021-08-20

Hi Gioele,

I think you could do this pretty easily by viewing the raw file in ProteoWizard's SeeMS program, and copying the values out of the table it presents.

Thanks for using the Skyline support board,

Brian Pratt

 
gioele visconti responded:  2021-08-23

Hi Brian,

Thank you for your answer and the information.

I can see the MRM functions with SeeMS but there is no information about the compound name, but "only" the information about the polarity, the precursor and the fragments (see SeeMS.png). Do you know if there is a way to extrapolate more information (like on the other image, see Desired_Transitions_list.png)?

Thanks again for your support.

Best regards,

Gioele

 
Brian Pratt responded:  2021-08-23
As far as I know, there is no such metadata in the raw file. Raw mass spec formats generally do not encompass compound identification metadata - none that I know of.

We have many, many Waters users, though, and this hasn't been a usability issue, so there's probably some step we're missing. Can you tell me more about the software in use leading up to creating that experiment file? At some point you presumably have a list of compounds and transitions of interest, getting that into Skyline is most likely already a solved problem.

Best regards,

Brian

 
gioele visconti responded:  2021-08-23
Hi Brian,

We are using MassLynx V4.2 SCN1012 and there is no way to export the MRM transitions (of functions, as they are called on the method editor) to a csv file.

I also contacted the Waters technical support and they told me that there is two workarounds to export MRM transitions: 1) print the method report as PDF and convert it as an Excel file; 2) open the raw file and click on "Experiment..." and copy paste the information (see pictures 1 and 2 on the first message).

Both methods are laborious and lot of lines/column needs to be cleaned before the table can be imported as a transition list into Skyline.

If other Waters users know how to do this step in a faster way it will be appreciated. Sometimes we have methods with lots of compounds and an automated way to import transitions list will help us a lot.

Thanks again and best regards,

Gioele

 
Brian Pratt responded:  2021-08-24
Hi Gioele,

Looking into this a bit deeper it seems I'm wrong about this not being an issue for other Waters users: https://skyline.ms/announcements/home/support/thread.view?rowId=38266

I would suggest looking through other Skyline support board queries to see what other Waters users have tried. One possible approach would be to compose your list of targets in Skyline, and export methods from there, but it sounds like even that has been problematic with MassLynx 4.2.

I'm sorry to pass the buck but I don't think this is a problem we can solve from our end - though we're certainly happy to work with you and anyone at Waters to resolve it.

Brian

 
gioele visconti responded:  2021-08-24
Hi Brian,

Thank you for your answer.

As I am doing targeted analysis I need to create and optimize MRM transitions using MassLynx. Then it is not useful for me to create the transition list in Skyline and import it in MassLynx. I was wondering if it was possible to implement in Skyline a feature that can read the MRM transitions list directly from RAW files (like SeeMS) and automatically create the transition list. I am asking this because for this kind of targeted approaches the information that Skyline needs to build a project (compound name, polarity, precursor m/z, fragments m/z, CE, etc) are in RAW files and an automation will be greatly appreciated in terms of productivity.

I will also contact the Waters technical support to ask if they can provide additional information on how to export the MRM transitions as a csv file.

Best regards,

Gioele

 
Brian Pratt responded:  2021-08-25
Hi Gioele,

To the best of my knowledge, MassLynx associates an experiment (and thus its compound and fragment names metadata) with one or more resulting raw mass spec data files, but those raw files do not themselves contain that metadata.

But perhaps I am mistaken, and you can provide an example of a raw file that does contain compound and fragment names metadata, and I can work with Waters to understand how to extract it (the raw file reader API they currently provide has no hint of that, though). You can upload to http://skyline.ms/files.url, or use any means of transfer that's convenient for you.

A method such as the kind Skyline generates for CE optimization does contain that kind of compound information, perhaps MassLynx produces such an artifact along the way? Again, I don't know enough about MassLynx to be really helpful, but it seems like there might be a intermediate file on your system that contains the desired information. Skyline can already directly read a number of native transition list formats. Though I rather think that if that was the case we'd be doing it already.

Let's do continue to work the problem - we certainly want science to proceed as efficiently as possible. But I think part of the answer is probably going to be customer pressure on Waters.

Best regards,

Brian

 
gioele visconti responded:  2021-08-26
Hello Brian,

Sure, I uploaded a RAW file on http://skyline.ms/files.url, the file is named 20210826_Gioele_MRM and the password to open the archive is uNigE2021. This RAW file contains 45 functions for 159 MRM, plus 2 Radar functions. This latter is a MS2 scan (Full Scan) performed to monitor the contaminant/matrix eluted during the chromatogram. All the functions are monitored for 25min.

So far, the Waters technical support is investigating on the possibility on how to export the MRM transition list. I will keep you update about possible a workaround on their side.

Thanks a lot for your support! Best regards,

Gioele
 
Brian Pratt responded:  2021-08-26
I have the file, thanks. I downloaded it and it's been removed from the server.

If indeed there is compound information embedded in there somewhere, what would it be? No need for a full list, but a few details would be helpful for search purposes.

I'm also double checking with a contact at Waters to confirm my understanding that any compound information is held in the MassLynx database that associates the raw files with the experiment, rather than in the raw files themselves.

Best regards,

Brian
 
gioele visconti responded:  2021-08-26
Hi Brian,

Attached you can find an Excel file (20210827_Gioele_MRM_transition_list.xlsx) with the information I would like to extract from the RAW file.

Let me know if you need additional information. Thanks for investigating that.

Best regards,

Gioele
 
Brian Pratt responded:  2021-08-27
Hi Gioele,

My contact at Waters confirms that .RAW files contain no compound metadata. He suggests, though, that the .exp file associated with your experiment should contain the metadata of interest. Let's have a look at that and see if it's decipherable, and whether we can correlate the contents to your transition list xlsx file.

Best regards,

Brian
 
gioele visconti responded:  2021-08-29
Hello Brian,

I uploaded the .exp file with the transitions that are contained into the previous Excel file (20210827_Gioele_MRM_transition_list.xlsx). You can find it on http://skyline.ms/files.url, the file is named 20210830_Gioele_MRM.zip and the password to open the archive is uNigE2021.

Let me know if you need additional information.Thanks for your help.

Best regards,

Gioele
 
Brian Pratt responded:  2021-08-30
I have the file, thanks. Unfortunately that's not a format that we can readily import, in that it's not column oriented.

Reviewing the known issues that I thought were related, I see that they were actually about Skyline exporting to MassLynx rather than the other way around, so it really does seem odd that this issue hasn't been raised before.

I'm curious to know what Waters customer support suggests. If there is a column oriented display in MassLynx that you can copy to the clipboard, you should be able to paste that directly into Skyline. It doesn't seem like you should have to pass it through a PDF export.

Best regards,

Brian
 
Brian Pratt responded:  2021-08-31
From a conversation with my contact at Waters, it sounds like you'd be better off using TargetLynx, which does present a table that you could readily use for copy/paste to Skyline.

It looks to me like it would also be a pretty simple matter for someone in your lab to write a small python script to extract the values in the .exp file and put them into a columnar format that Skyline could readily consume.

Best regards,

Brian
 
gioele visconti responded:  2021-08-31
Hi Brian,

Exactly I was quite surprised about the tedious way to export MRM transitions in a column-oriented display using MassLynx.

I got the same answer from Waters technical support, they suggest using another software that normally is included with TargetLynx (QuanPedia). This software is normally used as MRM database, you can also import the MS method to obtain the desired table as a query with SQLite.

This Friday we are going to perform an onsite training with an LC-MS application specialist from Waters that proposed the above-described procedure. I will keep you updated on the feasibility of this methodology.

Thanks for your help! Best regards,

Gioele