Hi,
There is not currently a way to add big Y ions to the spectral library, mostly because none of the tools we use that read the spectral libraries (DIA-NN, Skyline, etc.) currently support these ions.

But if you are just looking for the intensities of the Y ions from identified spectra, you can use the PTM-Shepherd diagnostic feature extraction module to get them by placing the masses (e.g., 203.079 for pep HexNAc) in the Peptide remainder fragments box. It generates a diagnosticIons.tsv file that shows the intensity of each provided ion for all PSMs - not a spectral library, but maybe useful depending on what you're trying to do.

Best,
Dan

Hi Dan,

Thank you so much for your information. I followed your instruction and it worked. There are two small questions following: 1, are the column names started with 'ox' in diagnosticlons.tsv are capital B ions? 2, the intensity values are quite small. Are they log2 scaled?

Yes, the columns starting with "ox" are B ions for glycans - it means an ion found as [M H] at the m/z listed in the column header.

And the intensity values are not log2, but rather relative intensity as a percentage of the base peak in the spectrum (so a value of 100 means it is the base peak). For the peptide remainder ions (Y ions), all charge states found are summed together, so it is possible to get a value greater than 100, meaning that the sum of the charge states for this ion was greater than the height of the base peak.

Best,
Dan

Hi Dan,

Got it. Thank you so much for your explanation. I will leave comments here if I have questions in the future. Thank you and your team members again for building this amazing software.

You are very welcome!