MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

Abstract

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. Graphical abstract ᅟ.

Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex

“…For data processing, the acquired MS spectra were visualized using Thermo Xcalibur Qual Browser (v. 4.2.47). MS spectra deconvolution was performed either manually or using the software UniDec v. 4.2.0 (Marty et al, 2015;Reid et al, 2019). The deconvolved spectra were replotted using the m/z software (Proteometrics LLC).…”

HIV-1 Gag protein with or without p6 specifically dimerizes on the viral RNA packaging signal

“…A minimum of three technical repeats were performed for each combination of Gag and RNA. Mass spectra were deconvolved using UniDec v4.1 (62,63). Theoretical molecular weights were calculated based on protein and RNA sequences (provided in Table S2) using the Protein/RNA molecular weight calculator tool in UniDec.…”

Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry

“…A recently incorporated module "MetaUniDec" also allows for highthroughput batch deconvolution of mass spectra. 26 UniDec is directly compatible with data collected on Thermo and Waters mass spectrometers, and indirectly compatible with other mass spectrometer brands by first converting the raw data to mzML, or .txt file format.…”