Hi, thanks for a great tool,
I have some questions about how different ion types are handled by the pipeline.
Reading the docs, it seems to me like there is no clear way of handling diagnostic fragments?
For example, peptides with PTMs may sometimes experience partial fragmentation of the modification, which results in a neutral loss (so a mass shift on the peptide backbone slightly smaller than for the intact PTM) but also the presence of the corresponding diagnostic ions from the fragmented PTM, which serve as evidence for its presence on the ion.
Is it currently possible to account for this situation with spectrum_utils? I know neutral losses are considered, but for the situation with PTMs it would be important to only consider this mass shift on fragments where the modification resides.
Second question, reading about the accepted ion types:
https://spectrum-utils.readthedocs.io/en/latest/annotating.html#ion-types
Does the tool take z-dot (sometimes called z+1) and z-dot-dot (z+2) type ions too? These are extremely common with ETD fragmentation where ions may have additional hydrogen atoms. I assume not since only z-ions are specified?
On this topic, ETD can also fragment the side-chains of amino acids (so called "satellite" ions).
https://www.matrixscience.com/help/fragmentation_help.html
https://www.matrixscience.com/blog/ion-series-for-ethcd.html
Particularly, the w-ion is helpful and can be quite prominent, resulting in fragmentation at the beta-carbon atom from a z-ion. Is there any possibility of including these ions in the future?
Thanks again, and I appreciate the great effort put into this tool already.
Best wishes,
Jonas Elsborg
Hi, thanks for a great tool,
I have some questions about how different ion types are handled by the pipeline.
Reading the docs, it seems to me like there is no clear way of handling diagnostic fragments?
For example, peptides with PTMs may sometimes experience partial fragmentation of the modification, which results in a neutral loss (so a mass shift on the peptide backbone slightly smaller than for the intact PTM) but also the presence of the corresponding diagnostic ions from the fragmented PTM, which serve as evidence for its presence on the ion.
Is it currently possible to account for this situation with spectrum_utils? I know neutral losses are considered, but for the situation with PTMs it would be important to only consider this mass shift on fragments where the modification resides.
Second question, reading about the accepted ion types:
https://spectrum-utils.readthedocs.io/en/latest/annotating.html#ion-types
Does the tool take z-dot (sometimes called z+1) and z-dot-dot (z+2) type ions too? These are extremely common with ETD fragmentation where ions may have additional hydrogen atoms. I assume not since only z-ions are specified?
On this topic, ETD can also fragment the side-chains of amino acids (so called "satellite" ions).
https://www.matrixscience.com/help/fragmentation_help.html
https://www.matrixscience.com/blog/ion-series-for-ethcd.html
Particularly, the w-ion is helpful and can be quite prominent, resulting in fragmentation at the beta-carbon atom from a z-ion. Is there any possibility of including these ions in the future?
Thanks again, and I appreciate the great effort put into this tool already.
Best wishes,
Jonas Elsborg