Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry-Based Proteomics

In bottom-up mass spectrometry-based proteomics, deep proteome coverage is limited by high cofragmentation rates. Cofragmentation occurs when more than one analyte is isolated by the quadrupole and the subsequent fragmentation event produces fragment ions of heterogeneous origin. One strategy to reduce cofragmentation rates is through effective peptide separation techniques such as chromatographic separation and, the more recently popularized, ion mobility (IM) spectrometry, which separates peptides by their collisional cross section. Here, we use a computational model to investigate the capability of the trapped IM spectrometry (TIMS) device at effectively separating peptide ions and quantify the separation power of the TIMS device in the context of a parallel accumulation-serial fragmentation (PASEF) workflow. We found that TIMS separation increases the number of interference-free MS1 peptide features 9.2-fold, while decreasing the average peptide density in precursor spectra 6.5-fold. In a data-dependent acquisition PASEF workflow, IM separation increases the number of spectra without cofragmentation by a factor of 4.1 and the number of high-quality spectra 17-fold. Using a categorical model, we estimate that this observed decrease in spectral complexity results in an increased likelihood for peptide spectral matches, which may improve peptide identification rates. In the context of a data-independent acquisition workflow, the reduction in spectral complexity resulting from IM separation is estimated to be equivalent to a 4-fold decrease in the isolation window width (from 25 to 6.5 Da). Our study demonstrates that TIMS separation decreases spectral complexity by reducing cofragmentation rates, suggesting that TIMS separation may contribute toward the high identification rates observed in PASEF workflows.

Automated summary

The study demonstrates that using TIMS device effectively separates peptide ions, reduces cofragmentation rates, and decreases spectral complexity, leading to improved quality of mass spectrometry data and protein identification rates.