Wrong annotation for EThCD and ETciD with last Tune v4.0

[rolivella]

Hello

I'm having an issue with the new Tune v4.0. After processing the raw files with the last TRFP version the CID part of ETciD is lost. For instance:

<activation>
  <cvParam cvRef="MS" accession="MS:1000045" value="88.6927185058594" name="collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
  <cvParam cvRef="MS" accession="MS:1000598" value="" name="electron transfer dissociation" />
</activation>

Another raw file but acquired with the old Tune v3.5 and the last TRFP version does not lose the CID part, has can be seen in this code:

<activation>
   <cvParam cvRef="MS" accession="MS:1000045" value="100.179542541504" name="collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
   <cvParam cvRef="MS" accession="MS:1000598" value="" name="electron transfer dissociation" />
   <cvParam cvRef="MS" accession="MS:1002680" value="35" name="supplemental collision energy" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
   <cvParam cvRef="MS" accession="MS:1002679" value="" name="supplemental collision-induced dissociation" />
</activation>

Could you please check? Here the mzMLs and RAWs: https://www.dropbox.com/scl/fo/06bn1v1a92xmxri1nsa36/h?rlkey=aeebgjt2ua3iuxdl58vhux4j3&dl=0

[caetera]

Hi @rolivella, Thank you for using TRFP. I can confirm the error. The reason for it is, however not clear. I can see that the parsing library (the Thermo one) indeed reports that the corresponding scans do not have supplemental activation, i.e. TRFP has nothing to do with it. I have access to another Eclipse running Tune 4.0.4084.22, I will try to get some EThcD runs from this instrument to check if the error can be reproduced.

[rolivella]

Hi @caetera thank you for taking care of this. Let me know if the error can be reproduced for EThcD. In that I case I will try to open an issue with the parsing library devs.

[caetera]

Hi @rolivella, I can confirm the same problem with files acquired on a different Eclipse. I am afraid the error stems not even from the parsing libraries, but from the Tune itself. Scan filter strings lack the sa flag, which is set for supplementary activation (on Tune < 4). I am not sure if this change was made for a reason, and, if not, why it has not been spotted yet by others.

@jshofstahl @jesse-canterbury, @chambm, do you know anything about this issue?

[rolivella]

OK @caetera I'll also discuss this issue with my teammates and let you know.

[rolivella]

Hi again, we checked a RAW file acquired with Tune 4.0.4091 and it has all the information at the header, so it means that is not an issue from Thermo's side:

[caetera]

Here is the comparison of two scan filters (scan 37) for the files you have shared.

Tune 3.5: ITMS + c NSI r d sa Full ms2 [email protected] [email protected] [100.0000-801.0000]

Tune 4.0: ITMS + c NSI r d Full ms2 [email protected] [email protected] [100.0000-985.0000]

The difference is sa that was previously used for all scans with supplemental activation and, I assume, is the reason why the libraries cannot detect it anymore. I am not sure if Thermo just changed the format of their scans without any warning, or if it is a bug of some kind. I will try to contact Thermo about it. On a side note, I can see that the latest version of MSConvert can not detect supplementary activation in Tune 4.x files as well, i.e. it is a general problem.

[jesse-canterbury]

Thanks for that last message with the scan filter comparison. I will ask internally and see what folks have to say about this.

[jesse-canterbury]

Hi all, we can see this is a bug on our side. We should be able to get this fixed for Tune 4.2, which should be released some time in the vicinity of ASMS '24. Thanks a lot for the report!

[caetera]

Thank you for the update @jesse-canterbury.

@rolivella As an immediate solution, I will need to change the code to allow parsing of the files with invalid scan headers and hope to come up with a beta soon.

[rolivella]

@caetera good, thank you very much!

[caetera]

Hi @rolivella, I have implemented a fix for the missing supplementary activation error. You can download and test the next beta version using this link: https://syddanskuni-my.sharepoint.com/:u:/g/personal/vgor_bmb_sdu_dk/EUq2DvQ3I_hEvf-N2_I3weUBCKeiRVeJNKv7sX0mmt2C7g?e=kRseht

[rolivella]

Thanks @caetera ! Is this version available at the biocontainer repo? I'm using the TRFP within a Nextflow pipeline in a linux environment...

[caetera]

The biocontainer repo will be updated only after the release, i.e. it will take some time more before it happens.