Deamidation is a polarizing issue. Some people throw it into their searches, other people don't. Dave Muddiman has a paper out there that shows that, a lot of times, what appears to be deamidation may simply be a search artifact. But there is a paper out there that I won't direct you to, that uses 1Da shifts on instruments that are not accurate mass to determine the presence or absence of glycosylation sites and it went into a really nice journal.
Piliang Hao et. al., took a real close look at deamidation of peptides treated with a number of various buffer conditions. To keep things simple, they start with a synthetic peptide, then they go up orders of magnitude in complexity and check out some iTRAQ labeled peptides from rat kidneys.
For the MS/MS analysis, they use a Q Exactive. The data processing was performed with custom Perl scripts, MaxQuant, and I think they used Mascot as well. In case you were wondering, deamidation was searched as a dynamic modification.
What did they find out? Its summed up pretty well in the charge above. I feel like I had a rant recently about how we need to start standardizing our sample prep methods, but it seems hazy now...
This is a nice short study that you can easily finish over a cup of coffee.
Is it possible to get a link to the paper using the inaccurate glycosylation determination? I would love to use it in an informal journal club, and am not, as you were not either, out to point finger at any specific group. I believe the biological field have a lot to learn from papers like this. We are not used to the accuracy or correct settings of the different mass spectrometers yet.
Keep up your work with the blog, it's very useful for us who are new to the field!
Marten, please send me an email: firstname.lastname@example.orgDelete