SWATH Quantification - Can ions be linked to proteins by mapping results to a theoretical database? Is this mapping done by MS/MS identification software?
Yes, once the IDA (Information Dependent Acquisition) is completed, the MS and MS/MS information for each ion is mapped to a theoretical database to identify the peptides and proteins present in the sample. This process can be accomplished using several algorithms, including Mascot, OMSSA, ProteinPilot, or multi-algorithm interfaces such as SearchGUI.
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