The UniDec Processing Pipeline for Rapid Analysis of Biotherapeutic Mass Spectrometry Data

10 May 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

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 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.

Keywords

UniDec
Native Mass Spectrometry
Biotherapeutics
Antibody-Drug Conjugates
Bispecific Antibodies
Mass Spectrometry Deconvolution

Supplementary materials

Title
Description
Actions
Title
Help File
Description
Help File with additional instructions and full listings of potential parameters.
Actions
Title
Example BsAb Report
Description
Example BsAb HTML report for a single file
Actions
Title
Example DAR Combined Report
Description
Example DAR combined report without DoubleDec
Actions
Title
Example DAR Report DoubleDec
Description
Example DAR Report with DoubleDec
Actions
Title
Example BsAb Input File
Description
Example input file for BsAb workflow
Actions
Title
Example BsAb Results File
Description
Example output results file for BsAb workflow
Actions
Title
Example DAR Results File
Description
Example of results (with inputs) for DAR workflow
Actions

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