Hello, I want to figure out the degraded product of a peptide (m.w.: >3500)). I did an LC-MS analysis and got a few degraded products (new mass). How can we get the formula or sequence of that degraded peptide from its mass (m/z)? Please share any online tools or materials that will be helpful.
Thank you.
With just the main peak, you won't be able to resolve that much. If you are lucky and the isotopic distribution is resolvable, you can determine the sum formula which will probably not be ultra helpful. Here's one possible software:
https://www.kofo.mpg.de/en/research/services/ms/research-topics/software-for-mass-spectrum-analysis
If you want to actually resolve the structure, that's a lot more work. From the mass spectral point of view, coupling in a cell for collision induced dissociation (CID) is one option to get to the sequence.
There's a reason why proteomics is a specialization field of its own, there is quite a lot of know-how required.
Hi Washim Khan,
you can try to compare the masses of the degraded peptides with the mass of their origin and try to evaluate the sequence of the missing region by comparison of the mass difference with in silico data from the non denatured peptide sequence and try to find matching masses to the in silico degradation products.
Best way to find the sequence of the degraded peptides would be to acquire MS2 fragmentation data wher u can possibly even do a manual readout of the sequence.
Best,
Murat
Dr. Washim, you may think about first N- and C- terminal clippings. Second one try to calculate the mass differences and annotate as per edman degradation/ pep seq
If the fragments are made from common amino acids, you can get the determine what amino acids are in a peptide by using their masses, and trying different combinations of amino acid masses until you get a match in your molecular ion peak. You won't get a sequence in this fashion. This is a task best done by computer.
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