nice to learn about these "wet" lab things as well, thanks! wondering what are the downstream impact on LC MS MS IDs? Is there an review article on what kinds and amounts of proteins one gets with different reagents and workflows in general?
The short answer is that anything in your sample that is NOT a peptide is going to affect your ID numbers and quantitative accuracy. Lipids often ionise better than peptides. I am not aware of a comprehensive review article about all of this. There is a good one about detergents (that I can't find right now). The other excellent resource is this: github.com/jessegmeyerlab/proteomics-tutorial. However, it does contain some omissions (like sulfonate based stage tips).
@@MatthewPadula thanks again for sharing which looks like a wonderful resource! i will surely take a look, meanwhile could these "impurities" be the reason that we see not-so-great correlation between DIA and DDA ID and Quant values?
@@AnimeshSharma1977 No. That's a different problem based in the way each of those methods acquire the data. The sample being analysed is almost always prepared in the same way.
nice to learn about these "wet" lab things as well, thanks! wondering what are the downstream impact on LC MS MS IDs? Is there an review article on what kinds and amounts of proteins one gets with different reagents and workflows in general?
The short answer is that anything in your sample that is NOT a peptide is going to affect your ID numbers and quantitative accuracy. Lipids often ionise better than peptides.
I am not aware of a comprehensive review article about all of this. There is a good one about detergents (that I can't find right now). The other excellent resource is this: github.com/jessegmeyerlab/proteomics-tutorial. However, it does contain some omissions (like sulfonate based stage tips).
@@MatthewPadula thanks again for sharing which looks like a wonderful resource! i will surely take a look, meanwhile could these "impurities" be the reason that we see not-so-great correlation between DIA and DDA ID and Quant values?
@@AnimeshSharma1977 No. That's a different problem based in the way each of those methods acquire the data. The sample being analysed is almost always prepared in the same way.