We've have peptide retention time in silico predictors for at least 15 years - and sometimes they work great. I don't think it is controversial at all to say that real peptide standards work better.
This recent Open Access Paper takes a look at the difference between the two -- as well as different retention time calibration mathematical models in the context of SWATH and DIA.
And the results are pretty clear from their work -- in DIA it helps a lot to have retention time control for your identifications. With the added uncertainty of the bigger windows or having the MS1 for quan that is not directly linked by the instrument to the MS/MS fragments -- this is really valuable.
Also, this paper is great because it highlights how ridiculously great the Q Exactive Classic is for DIA. They can get over 10% more protein IDs with their high precision iRT model, pushing standard 2 hour DIA on human digests from 4,500 protein groups up to 5,000 protein groups!
5,000 protein groups in 2 hours from human digest!!!!! I need to do more DIA....
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