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QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure

Overview of attention for article published in BMC Bioinformatics, December 2014
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Title
QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure
Published in
BMC Bioinformatics, December 2014
DOI 10.1186/s12859-014-0403-1
Pubmed ID
Authors

Joseph P Salisbury, Qian Liu, Jeffrey N Agar

Abstract

BackgroundHydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.ResultsHere, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.ConclusionIsotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.

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Mendeley readers

The data shown below were compiled from readership statistics for 23 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 4%
Unknown 22 96%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 30%
Student > Ph. D. Student 6 26%
Other 3 13%
Student > Bachelor 2 9%
Professor 1 4%
Other 2 9%
Unknown 2 9%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 26%
Chemistry 5 22%
Agricultural and Biological Sciences 4 17%
Computer Science 2 9%
Engineering 2 9%
Other 1 4%
Unknown 3 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 December 2014.
All research outputs
#11,069,166
of 14,573,111 outputs
Outputs from BMC Bioinformatics
#4,191
of 5,420 outputs
Outputs of similar age
#186,778
of 301,308 outputs
Outputs of similar age from BMC Bioinformatics
#251
of 320 outputs
Altmetric has tracked 14,573,111 research outputs across all sources so far. This one is in the 20th percentile – i.e., 20% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,420 research outputs from this source. They receive a mean Attention Score of 4.9. This one is in the 17th percentile – i.e., 17% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 301,308 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 320 others from the same source and published within six weeks on either side of this one. This one is in the 17th percentile – i.e., 17% of its contemporaries scored the same or lower than it.