1P-03 PDF
Improving Protein Sequence Coverage and Identification of Oxidation Sites via Top/Middle -Down Fragmentation and Ion-mobility Time-of-flight Mass Spectrometry
Direct fragmentation of intact proteins (Top-down) or protein sub-units (Middle-down) to obtain sequence information is emerging as a viable option in protein analysis. However, fragmentation of large therapeutic proteins tends to generate many different types (and charge states) of fragment ions, making the spectra interpretation and sequence deduction very challenging. Here we are reporting how mobility could be used in top/middle down experiment to simplify complex MS/MS spectra allowing better data interpretation. An informatics workflow was developed to allow us to systematically evaluate the performance difference in sequence coverage for therapeutic proteins with or without the use of ion-mobility separation. The developed workflow was used to characterize trastuzumab sub-units and oxidized intact human growth hormone (hGH).