MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

Deseree J. Reid, Jessica M. Diesing, Matthew A. Miller, Scott M. Perry, Jessica A. Wales, William "Bill" Montfort, Michael T. Marty

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)118-127
Number of pages10
JournalJournal of the American Society for Mass Spectrometry
Volume30
Issue number1
DOIs
StatePublished - Jan 1 2019

Fingerprint

Deconvolution
Throughput
Heme
Mass spectrometry
Mass Spectrometry
Software
Visualization
Chemical activation
Hemeproteins
Architectural Accessibility
Bacterial Proteins
Electric potential
Mass spectrometers
Graphical user interfaces
Lipoproteins
Industrial applications
Carrier Proteins
Nitric Oxide
Proteins
Oxygen

Keywords

  • Collision-induced dissociation
  • Deconvolution
  • Heme proteins
  • Nanodiscs
  • Native mass spectrometry

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy

Cite this

MetaUniDec : High-Throughput Deconvolution of Native Mass Spectra. / Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William "Bill"; Marty, Michael T.

In: Journal of the American Society for Mass Spectrometry, Vol. 30, No. 1, 01.01.2019, p. 118-127.

Research output: Contribution to journalArticle

Reid, Deseree J. ; Diesing, Jessica M. ; Miller, Matthew A. ; Perry, Scott M. ; Wales, Jessica A. ; Montfort, William "Bill" ; Marty, Michael T. / MetaUniDec : High-Throughput Deconvolution of Native Mass Spectra. In: Journal of the American Society for Mass Spectrometry. 2019 ; Vol. 30, No. 1. pp. 118-127.
@article{252d020d6dc74962ad903548648e11a4,
title = "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.",
keywords = "Collision-induced dissociation, Deconvolution, Heme proteins, Nanodiscs, Native mass spectrometry",
author = "Reid, {Deseree J.} and Diesing, {Jessica M.} and Miller, {Matthew A.} and Perry, {Scott M.} and Wales, {Jessica A.} and Montfort, {William {"}Bill{"}} and Marty, {Michael T.}",
year = "2019",
month = "1",
day = "1",
doi = "10.1007/s13361-018-1951-9",
language = "English (US)",
volume = "30",
pages = "118--127",
journal = "Journal of the American Society for Mass Spectrometry",
issn = "1044-0305",
publisher = "Springer New York",
number = "1",

}

TY - JOUR

T1 - MetaUniDec

T2 - High-Throughput Deconvolution of Native Mass Spectra

AU - Reid, Deseree J.

AU - Diesing, Jessica M.

AU - Miller, Matthew A.

AU - Perry, Scott M.

AU - Wales, Jessica A.

AU - Montfort, William "Bill"

AU - Marty, Michael T.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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.

KW - Collision-induced dissociation

KW - Deconvolution

KW - Heme proteins

KW - Nanodiscs

KW - Native mass spectrometry

UR - http://www.scopus.com/inward/record.url?scp=85053203354&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85053203354&partnerID=8YFLogxK

U2 - 10.1007/s13361-018-1951-9

DO - 10.1007/s13361-018-1951-9

M3 - Article

C2 - 29667162

AN - SCOPUS:85053203354

VL - 30

SP - 118

EP - 127

JO - Journal of the American Society for Mass Spectrometry

JF - Journal of the American Society for Mass Spectrometry

SN - 1044-0305

IS - 1

ER -