Discerning ambiguous internal fragment assignments that are generated in top-down mass spectrometry with cyclic ion-mobility enhances protein sequence information

Top-down mass spectrometry (TD-MS) has become a central technique for the analysis of intact proteins, and internal fragments (fragments containing neither the C- nor N-terminus) have been utilized to enhance the sequence information extracted from such experiments. A key obstacle to including internal fragments in TD-MS workflows stems from potential ambiguities in their assignments, which can severely impact the confidence of assignments and increase false discovery. To utilize internal fragments in TD-MS precisely, it is therefore crucial to discern ambiguous internal fragment assignments. Here, we demonstrate that by including ion mobility, ambiguous internal fragments can be discerned to enable more confident assignments. For example, the β-Casein-derived internal fragments a115¬-x132 and a114¬-x131 were both assigned to 1000.51 m/z; however, ion mobility of this m/z showed two different arrival time distributions: 25.5 ms and 30.0 ms. The different theoretical volumes of a115¬-x132 and a114¬-x131 – 680.6 and 682.3 respectively – enabled their assignments to the respective 25.5 ms and 30.0 ms arrival times. For the test proteins myoglobin, carbonic anhydrase II, β-Casein, and bovine serum albumin, the inclusion of ion mobility discerned internal fragments increased sequence coverage from <55% to >85%, which is near complete sequence coverage for these proteins. By applying this method to a protein complex, trustuzamab, the sequence coverage and sequence information returned for both the heavy and light chains were 85% and 90% respectively. These data demonstrate that the inclusion of ion mobility in TD-MS experiments can enhance the confidence of internal fragment assignments, and significantly extend protein sequence information relative to TD-MS experiments that do not incorporate ion mobility.