|Is Skyline appropriate for my purposes? Need help detecting small molecule modifications of cysteine residues||mschne08||2023-03-28|
I am very new to proteomics and am trying to decide if using Skyline is appropriate for the purposes of my experiments, and if so, how I would be able to effectively use it. My project currently revolves around detecting electrophilic small molecule modifications of cysteine residues in a purified protein.
I am currently using a bottom-up approach, digesting the protein and analyzing it in a data-dependent acquisition mode on a QTOF 5600. So far I have only been attempting to obtain good sequence coverage and to ensure that I see all of the cysteine-containing peptides appropriately labeled with iodoacetamide.
Moving forward, I will be using less common small molecule electrophiles that are hypothesized to favorably react with specific cysteine residues in the protein. The idea is that as I treat my protein with decreasing concentrations of these small molecules, fewer and fewer cysteines will be modified
In my first experiment, I treated my protein with the small molecule sulforaphane (monoisotopic mass of 177.0282). I followed the DDA search for MS1 filtering tutorial and the working with modifications webinar, but I'm still unsure if I'm using Skyline to its fullest capabilities, given that all of this is so new to me.
So, does Skyline seem appropriate to use for my experiments? If so, are there any recommendations as to how I could use it effectively?
If this kind of question is beyond the scope of this support board or if there is a better place to ask it, please let me know.
Thanks for your time!