30-50% of MS spectrums are detected from Tissue or Cell samples are unmatched with the available protein sequence database?
Can anyone suggest a methodological flow for this problem.
Thanks!
Did you perform any SDS-PAGE or Blotting before Mass spectra?
If you performed electrophoresis, after visuvalization of clear band you can use the samples for MS. For MS purity of sample is most important. Even after you could not get the result from exisiting protein database further you can go crystallographic studies. Because the samples from diseased human/animal tissue has more impurities (mutation). Abbas Khan
Hi Abbas,
It is not unusual to confirm your finding. This is due to the many many modified peptides/proteins that we do not account for during our efforts to match spectra to a protein sequence.
A very very common post translational modification for proteins is N-terminal acetylation (it adds 42 daltons to the mass of the peptide). Therefore, when I am searching MS/MS data, I use "acetyl N-terminal protein" as a variable modification. Another common modification see is the oxidation of methionine amino acid. I would also include this modification (it introduces 16daltons to the actual mass of the peptide)
In summary, the reason why we can never hope to account or to match all of our MS/MS spectra is due to the many many modified peptides that are fragmented during the LC-MS/MS analysis.
Best,
Hediye.
Gurudeeban Selvaraj Hediye Erdjument-Bromage Thank you very much for your valuable suggestions.
- Badges
- Science method
- Similar topics
- Methodology