MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

  • Deseree J. Reid
  • Jessica M. Diesing
  • Matthew A. Miller
  • Scott M. Perry
  • Jessica A. Wales
  • William R. Montfort
  • Michael T. MartyEmail author
Focus: Honoring Carol V. Robinson's Election to the National Academy of Sciences: Research Article


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


Native mass spectrometry Deconvolution Nanodiscs Heme proteins Collision-induced dissociation 



The authors thank Maria Reinhardt-Szyba and Alexander Makarov at Thermo Fisher Scientific for helpful discussions and support on the UHMR modification of the Q-Exactive HF instrument. The pMSP1D1 plasmid was a gift from Stephen Sligar (Addgene plasmid no. 20061). This work was funded by an American Cancer Society Institutional Research Grant (IRG-16-124-37-IRG) and the Bisgrove Scholar Award from Science Foundation Arizona to M.T.M.; by National Institutes of Health grants R01 GM117357 and P30 CA023074 to W.R.M. and T32 GM008804 to J.W.; and American Heart Association grant 16PRE31090034 to J.W.

Supplementary material

13361_2018_1951_MOESM1_ESM.pdf (270 kb)
ESM 1 (PDF 270 kb)


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© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of ArizonaTucsonUSA

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