For targeted processing of SWATH acquisition proteomics data, ion libraries are used to provide the information on the proteins, peptides, fragment ions and retention time to be used. To get the most out of your SWATH acquisition data, it is often required to build larger ion libraries. The ability to merge multiple proteomic ion libraries is now included in the Extractor App in OneOmics suite.
When defining your Extractor job, you will select 1 or more ion libraries for processing. If more than 1 is selected a library merge will be performed. First the library with the most number of compounds is selected as the Seed library. The other libraries are then merged into this reference library using a non-linear retention time alignment algorithm. There must be at least 100 peptides found that overlap with the Seed library for a new library to get merged in. When overlapping proteins are found between libraries, the peptide with the highest ID confidence will be used in the final library, and any new peptides from the added libraries will get added to the protein.