UniDec Processing Pipeline for Rapid Analysis of Biotherapeutic Mass Spectrometry Data

Recent advances in native mass spectrometry (MS) and
denatured
intact protein MS have made these techniques essential for biotherapeutic
characterization. As MS analysis has increased in throughput and scale,
new data analysis workflows are needed to provide rapid quantitation
from large datasets. Here, we describe the UniDec processing pipeline
(UPP) for the analysis of batched biotherapeutic intact MS data. UPP
is built into the UniDec software package, which provides fast processing,
deconvolution, and peak detection. The user and programming interfaces
for UPP read a spreadsheet that contains the data file names, deconvolution
parameters, and quantitation settings. After iterating through the
spreadsheet and analyzing each file, it returns a spreadsheet of results
and HTML reports. We demonstrate the use of UPP to measure the correct
pairing percentage on a set of bispecific antibody data and to measure
drug-to-antibody ratios from antibody–drug conjugates. Moreover,
because the software is free and open-source, users can easily build
on this platform to create customized workflows and calculations.
Thus, UPP provides a flexible workflow that can be deployed in diverse
settings and for a wide range of biotherapeutic applications.