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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 data, it is often required to build larger ion libraries. The ability to merge multiple proteomic ion libraries is now included in the OneOmics™ Extractor application.
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.
RUO-MKT-18-6401-A
Posted October 8, 2018 at 9:59 PM by chuen Lam
Dear Christie,
I'm wondering if the same merging algorithm is being used in the Proteinpilot (PP) desktop ver when multiple DDA files are added for a combined search? The algorithm implemented on the OneOmics makes sense to me but it seems that no explanation is given for PP regarding how multiple files are integrated. From my experience, when there are too many DDA files combined to generate a bigger library in PP, the CV for SWATH extraction becomes worse. Thanks.