Fast and Accurate Charge State Deconvolution of Protein Mass Spectra

Charge state deconvolution is essential for efficient
and effective
protein mass spectrometry analysis. High-quality mass profiling is
necessary to determine which proteoforms are present in protein samples
and their relative abundances. In the pursuit of a well-rounded deconvolution
solution, we detail an iterative charge state deconvolution algorithm
named kDecon that has been tuned to provide high accuracy in its mass
results while also delivering superb sensitivity toward lower abundance
proteoforms in complex spectra. Here, the performance of kDecon as
a mass determination algorithm for both targeted antibody and high-throughput
proteomics analysis was benchmarked against existing deconvolution
solutions. While the different deconvolution routines all proved robust
for detecting the highest abundance protein species, kDecon ultimately
showcased best-in-class precision for lower abundance proteoform mass
profiling. Furthermore, kDecon results had up to 7-fold fewer false
positives and simultaneously exhibited at least 20-fold speed improvements
over the other algorithms. Overall, these deconvolution advances will
contribute to enabling both routine and thorough intact mass profiling
studies for biotherapeutics as well as improving the proteome coverage
of top-down proteomics experiments.