Problems with import of peak boundaries in smallmolecule mode for .wiff data

Problems with import of peak boundaries in smallmolecule mode for .wiff data Max  2020-08-24


i am trying to import peak boundaries for a number of data sets based on .wiff data. We have set up some small molecule transitions for small molecules and peptides (due to qunatifiaction porpuses). I have used the allready discussed workarounds for small molecules (see which is perfectly working for data from e.g. waters were a single filne represents a single injection. However, in the case of AbSciex 5500 the data is stored in a single .wiff file. I added therefore the sample name (alias Sample identifier) column to the peak boundaries list as stated in the FAQ for importing peak boundaries (see here: Nevertheless, skyline gives me an error message back stating that the sample names are not fitting to the sample names in the raw file . We have not changed the names of the single sample upon importing in Skyline thus i am looking for help to resolve this. I know i am missing something but i can not figure it out....

Looking forward to hear from you guys!


PS: I have example files ready but can only send them confidentally.

Nick Shulman responded:  2020-08-24
In the peak boundaries CSV file, the column containing the WIFF sample name is supposed to be called:
or also it is allowed to have a space in it:
Sample Name

Is that what you have named that column in your peak boundaries file?

It sounds like you are getting the error message that says:
Sample <something> on line <somethingelse> does not match the file <anotherthing>.

I will send you an email message and we can figure out how you can send us your files so that we can figure out what is going wrong.
-- Nick
Nick Shulman responded:  2020-08-25

Thank you for sending me your data files.
This seems to be a bug in Skyline. Skyline can only handle multi-sample wiff files in peak boundary import if all of the samples from a particular wiff file are in the same replicate.
That is, Skyline sees the file name and then looks at the first replicate that contains that file, and expects to be able to find that sample within that particular replicate.
Instead, Skyline should look through all of the replicates trying to find a single Result File whose file name and sample name match what has been specified.

I cannot think of any workaround for this. I will try to fix this bug in Skyline-Daily soon.
-- Nick
Max responded:  2020-10-15
Hi Nick,

i just wanted to know if you already had time to address the issue?
Thanks for the continous development of this neat tool!

- Max
Nick Shulman responded:  2020-10-15

Thank you for reminding me. I will try to fix this in Skyline-Daily soon.
-- Nick