Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics

The most common data collection in shotgun proteomics is via data-dependent acquisition (DDA), a process driven by an automated instrument control routine that directs MS/MS acquisition from the highest abundant signals to the lowest. An alternative to DDA is data-independent acquisition (DIA), a process in which a specified range in m/z is fragmented without regard to prioritization of a precursor ion or its relative abundance in the mass spectrum, thus potentially offering a more comprehensive analysis of peptides than DDA. In this work, we evaluate both DDA and DIA on three different linear ion trap instruments: an LTQ, an LTQ modified with an electrodynamic ion funnel, and an LTQ Velos. These instruments represent both older (LTQ) and newer (LTQ Velos) ion trap designs (i.e., linear versus dual ion traps, respectively), and allow direct comparison of peptide identifications using both DDA and DIA analysis. Further, as the LTQ Velos has an enhanced "S-lens" ion guide to improve ion flux, we found it logical to determine if the former LTQ model could be leveraged by improving sensitivity by modifying with an electrodynamic ion guide of significantly different design to the S-lens. We find that the ion funnel enabled LTQ identifies more proteins in the insoluble fraction of a yeast lysate than the other two instruments in DIA mode, whereas the faster scanning LTQ Velos performs better in DDA mode. We explore reasons for these results, including differences in scan speed, source ion optics, and linear ion trap design.