Proteomic Profile of Daphnia pulex using Data-Independent Acquisition Mass Spectrometry and Ion Mobility Separation

In this study, various sample preparation and mass spectrometry acquisition methods were performed for the purpose of improving Daphnia pulex proteome exploration. We observed benefits for employing both in-gel and in-solution methods of trypsin digestion. Furthermore, data independent acquisition methods employing ion-mobility separation greatly increased peptide identification and more than doubled our proteome coverage.