Dear Skyline Support Team,
I am writing to report an issue I encountered when importing a .csv transition list containing light and heavy fragment ions.
Specifically, for certain compounds like labelled internal standards or halogenated compounds, I would like to monitor isotopologue fragment ions. In my .csv file, I have distinct entries for each species. For example, for 13C4-PFOA_H in the attached file (lines 272 and 273), I include the fragments C3F7[M-] (168.98937) and C'3F7[M-] (171.99944). However, when importing the transition list, only the light fragment is added to the target list, while the heavy fragment can only be added manually within Skyline. Could you confirm if this is a bug or if I am missing a step in the import process?
Additionally, I would greatly appreciate guidance on how to properly indicate adducts for heavy species within the same compound name. For example, for PFBA (lines 5 and 7), I can easily define [M-H] and [M-COOH] adducts directly from the molecular formula. However, for heavy species (lines 264 and 265), I have been naming them _H and _COOH, as I haven't found the appropriate nomenclature for indicating heavy isotope losses. Is there a recommended way to label these, e.g., something like [M-(13C)OOH], to display both precursors under the same compound?
I am using Skyline (64-bit) 24.1.0.199 (6a0775ef83) on Windows 10 64-bit. I have attached the .csv file used to create the target list.
Thank you for your time and assistance.
Best regards,
Francisco José |
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| Nick Shulman responded: |
2024-10-16 08:54 |
You can find some documentation for heavy labeled adducts here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=adduct_descriptions
Usually, in your transition list, the light and heavy items would have exactly the same "Molecule List Name", "Molecule Name" and, I believe, even "Molecular Formula".
The Precursor Adduct for the heavy precursors would have something extra on them to indicate the heavy label.
In your attached transition list, the lines for heavy items have a different Molecule List Name and Molecule Name which means that Skyline thinks they are separate molecules.
You would like Skyline to see your heavy transitions as belonging to the same molecule as the light transitions, just with a different Precursor Adduct. In that way, both the light and heavy chromatograms will be looked at when detecting and choosing chromatogram peaks.
-- Nick |
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| diaz-galiano responded: |
2024-10-17 00:08 |
Thank you for taking the time to look into this matter, Nick.
So, as I understand it, it is not currently possible to include both light and heavy fragments from a .csv transition list under the same molecule name? Leaving aside native and isotopically labelled compounds, I am also thinking about halogenated species. For instance, I would like to monitor both 35Cl and 37Cl fragments for the compound in lines 172 & 173. As mentioned before, I can add the 37Cl-containing fragment manually to the light precursor ion, but not via the transition list import. Is it compulsory for me to include the 37Cl precursor separately in my .csv if I want Skyline to include the heavy fragment, or is there no way to have it add the 37Cl fragment to the 35Cl precursor alongside the 35Cl fragment?
On another note, I had already gone through the adduct description page before posting. I have no issues creating ions based on de/protonations; however, I have not been successful in generating a decarboxylation ion for a 13C-labelled species (see the two lines below):
For the [M-H] adduct, Skyline automatically generates the [M4C13-H] precursor, which works as intended. However, for the decarboxylated ion, I have tried various adduct descriptions (such as [M4C13-COOH] and [M4C13-C'OOH]) without success. That is why, for now, I have resorted to manually removing 13COOH from the molecular formula and including it as a separate precursor. I didn’t find any examples of 13C-heavy isotope adducts with the loss of 13C atoms from the ion on the site, so this is probably straightforward, but I seem to be making a mistake in the syntax for those adducts.
Best regards,
Francisco José
Molecule List Name,Molecule Name,Precursor m/z,Molecular Formula,Exact Mass,Precursor Adduct,Precursor Charge,Product m/z,Product Formula,Product Adduct,Product Charge,Explicit Retention Time,Explicit Retention Time Window,CAS,SMILES,"InChI"
PFAS_Labelled,13C4-PFBA_H,,C'4HF7O2,217.999896017645,[M-H],-1,171.999435,C'3F7,[M-],-1,3.5,0.5,1017281-29-6,[13C](=O)([13C]([13C]([13C](F)(F)F)(F)F)(F)F)O ,"InChI=1S/C4HF7O2/c5-2(6,1(12)13)3(7,8)4(9,10)11/h(H,12,13)/i1+1,2+1,3+1,4+1 "
PFAS_Labelled,13C4-PFBA_COOH,,C'3F7-,171.99944,[M-],-1,69.999115,C'F3,[M-],-1,3.5,0.5,1017281-29-6,[13C](=O)([13C]([13C]([13C](F)(F)F)(F)F)(F)F)O ,"InChI=1S/C4HF7O2/c5-2(6,1(12)13)3(7,8)4(9,10)11/h(H,12,13)/i1+1,2+1,3+1,4+1 " |
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| Brian Pratt responded: |
2024-10-17 09:17 |
Hi Francisco:
I think this is what you want. The key is that the molecule-level values are the same, the differences are in the Precursor Adduct and fragment details.
Molecule List Name,Molecule Name,Precursor m/z,Molecular Formula,Exact Mass,Precursor Adduct,Precursor Charge,Product m/z,Product Formula,Product Adduct,Product Charge,Explicit Retention Time,Explicit Retention Time Window,CAS,SMILES,InChI
PFAS_Labelled,13C4-PFBA,,C4HF7O2,217.999896,[M4C13-H],-1,171.999435,C'3F7,[M-],-1,3.5,0.5,1017281-29-6,[13C](=O)([13C]([13C]([13C](F)(F)F)(F)F)(F)F)O ,"InChI=1S/C4HF7O2/c5-2(6,1(12)13)3(7,8)4(9,10)11/h(H,12,13)/i1+1,2+1,3+1,4+1 "
PFAS_Labelled,13C4-PFBA,,C4HF7O2,171.99944,[M3C13-COOH],-1,69.999115,C'F3,[M-],-1,3.5,0.5,1017281-29-6,[13C](=O)([13C]([13C]([13C](F)(F)F)(F)F)(F)F)O ,"InChI=1S/C4HF7O2/c5-2(6,1(12)13)3(7,8)4(9,10)11/h(H,12,13)/i1+1,2+1,3+1,4+1 "
I've attached a screenshot of Skyline with this transition list loaded.
Thanks for using the Skyline support board,
Brian Pratt |
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| Brian Pratt responded: |
2024-10-17 09:26 |
Actually just "PFBA" is a more sensible molecule name - didn't mean to leave the label stuff in there. |
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pfas_complete_precursor_01.csv
Screenshot 2024-10-17 091502.png