how to import TraML file into skyline?

how to import TraML file into skyline? caixue  2019-06-11

Is there any way to import TraML file into skyline? I have failed to import TraML or csv which from TraML file into skyline.
Thank you in advance!

best regards.
Xue Cai

Brendan MacLean responded:  2019-06-11

Hi Xue Cai,
We don't have support for importing TraML directly but you should be able to import the CSV file through File > Import > Assay Library.

What kind of failures are you getting? What is the source of your TraML? How was it created?

If you post your CSV file to our file drop point, I can have a look at it:

Thanks for your interest in using Skyline in your research.


caixue responded:  2019-06-11

Hi Brendan,
I failed to import CSV file > Import > Assay Library. The attachment is the error message, and I had posted my CSV file named UK_plasma_2013522_Noiso_Uniprotsemi_p085PlusPHL2Plasm_20131219 to your file drop point. Please refer to it.
Thank you for your patient reply.
Best wishes.
Xue Cai

Brendan MacLean responded:  2019-06-11

Well, it does look like we last updated unimod.xml in November 2017 but to a version that contains changes only up to 3/10/2017. And it looks like Unimod ID #35 (Oxidation) was most recently updated on 10/6/2017 to add a number of new amino acid residues including S:

 <umod:mod title="Oxidation" full_name="Oxidation or Hydroxylation"
            date_time_posted="2002-08-19 19:17:11"
            date_time_modified="2017-10-06 17:05:11"
     <umod:specificity hidden="1" site="T" position="Anywhere" classification="Chemical derivative"
     <umod:specificity hidden="1" site="E" position="Anywhere" classification="Chemical derivative"
        <umod:misc_notes>hydroxyglutamic acid</umod:misc_notes>
     <umod:specificity hidden="1" site="S" position="Anywhere" classification="Chemical derivative"
     <umod:specificity hidden="1" site="Q" position="Anywhere" classification="Chemical derivative"
     <umod:specificity hidden="1" site="L" position="Anywhere" classification="Chemical derivative"
     <umod:specificity hidden="1" site="I" position="Anywhere" classification="Chemical derivative"
     <umod:specificity hidden="1" site="U" position="Anywhere" classification="Multiple"
     <umod:specificity hidden="1" site="G" position="Any C-term" classification="Pre-translational"
        <umod:misc_notes>Hydroxyglycine derivative in amidation pathway</umod:misc_notes>

We will look into updating our unimod.xml file, but for now, you could also remove the offending rows from the CSV file that include S(UniMod:35). Hopefully, S oxidation is not an important target for you.

Sorry for falling behind this library. Thanks for letting us know it is time to do another update.


caixue responded:  2019-06-13

Hi Brendan,
Thank you so much for your suggestion. I had remove the offending rows from the CSV file, but there are also some error in other rows. Finally, I deleted all rows in question, and import a part of CSV file to the skyline. I really hope TraML file can be imported directely to skyline. Thanks so much.
Best wishes.
Xue Cai