i would like to know how fragments of a compound or bio molecule would appear on the MS graph if these fragments have equal m/z?
Basically, it depends on the MS analyzer resolution. On one hand, if the analyzer has unit resolution and there two or more compounds with same m/z, you will see just one peak. On the other hand, with an analyzer which perform high resolution measurements, one can separate the ions. Another possibility is to carry out Ion Mobility - mass spectrometry experiments. You can separate molecules based on collision cross section. Of course it depends on molecule structures.
I am re-interpreting your question a little to what I think you are asking: Two different molecules of the same m/z can be identified by fragmentation - they will break in a pattern determined by the distripution of molecular forces holding the parent molecule together - so PSD, of collision induced fragmentation MS will give a spectral pattern characteristic of the parent. If you have two fragments with identical M/Z this can be resolved by repeat fragmentation (ms/ms/ms or msn
You will see one peak only. This is the case for example for a mixture of two or more isomers. There are two or more compounds with the same molecular weight, but you will see only one peak, because m/z is the same. There is now way to separate the signals with the same value on MS.
Depends on the resolution of your mass analyzer and if "equal m/z" extends all the way to the decimals. The same nominal mass can often be differentiated in the decimals, as long as you do not have the exact same elemental composition. Look for m/z calculators on the web, there are some freely accessible where you can model spectra based on composition.
Many thanks to u all.Dear Lenz,yap my query was for those two molecules with same elemental composition.hypothetically,what if a peptide has two residues of a single amino acid?
If you had two peptides with the same amino-acid compositions but with different sequences, for example, YLYEIAR and YYLEIAR, the MS spectra, i.e., the protonated (and probably the diprotonated) signals would be at exactly the same m/z values. The peptides might have different LC retention times, but the single-analyzer mass spectra (MS not MS/MS) wouldn't distinguish them, even with high-resolution instruments. MS/MS spectra, however, would readily tell you which was which. Check out this set of handy basic calculators:
http://db.systemsbiology.net:8080/proteomicsToolkit/
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