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In this research paper they talk about the methylation of histone. They use mass spectrometry to identify which peptide position is methylated. Does the number yielded by the spectrometer calculate the mass of the amino acid with and without the mass of methyl group? I wonder because I saw some introduction saying the number present the molecular mass of the molecular. I also would like to ask the mechanism of it and how you interpret this data? Thank you!

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It is not simple MS, it is tandem MS. They send the sample through multiple MS and they fragment it between them. So they can get info about the molecular structure as well, not just the mass/charge of the molecule.

A quote from your article:

MS/MS spectra of the methylated H3 protein (top down) and fragments upon electron transfer dissociation fragmentation. Fragments of the methylated H3 have a mass shift of 42 starting at C14, indicating a modification site at the K14 at the N terminus of the peptide. Normalized collision energy = 35%, activation Q = 0.250, activation time = 100 ms, accumulation time = 5 min.

A reference from your article:

Frese et al., 2011 C.K. Frese, A.F. Altelaar, M.L. Hennrich, D. Nolting, M. Zeller, J. Griep-Raming, A.J. Heck, S. Mohammed

Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos

J. Proteome Res., 10 (2011), pp. 2377–2388

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The numbers yielded by any mass spectrometer are always the mass divided by charge (m/z).

Figure 2B in the paper shows the peaks from a peptide that was isolated and then fragmented inside the mass spectrometer. The ideal scenario is that each peak has an m/z that corresponds to a potential fragment of the peptide (or whatever is being analysed).

The fragment ions that indicate the methylation include the monoisotopic mass of three methyl groups (~42). These ions (C14 - C21) also carried two electrons. The machine provides m/z so add the monoisotopic mass of peptide + monoisotopic mass of three methyl groups + mass of two electrons and then divide by the charge (2).

The effect of the charge state can be seen when you look at C13(+;1360.79 m/z) and C14(++;766 m/z).

I didn't know how to address the "mechanism of it".

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